Let me just respond to this, I've been advocating for Garchomp to move up for a couple of months. This isn't fair, Manaphy, Charizard-X and Clefable have no counters, true. They can tweak their set to beat any mon... But Garchomp can do this as well... It's sheer versatility makes it very hard to switch in and revenge kill. Mentioning Keldeo, Latios and Mega Mane is kind of silly, when Sub-Salac beats all three of them, or did you just forget about that set? It's not just that it has a large variation of sets to choose from, it also has multiple options to its sets. Wether it's tankchomp, who can run toxic, stone edge, fire blast ect as options. Scarf running stone edge, outrage, fire blast. SD running substitute, stone edge, iron head ect to handle what it wants to handle. There is no 100% counter to any of Garchomps sets.
252 Atk Life Orb Garchomp Earthquake vs. 248 HP / 252+ Def Clefable: 187-222 (47.5 - 56.4%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
Even Clefable isn't safe.
When comparing Chomp to other S Rank mons, and saying that it can also 'tweak' its set to beat anything, people tend to miss the vital distinction between 'tweaking' the same set and running different sets altogether. You're right, that the S Rank mons can tweak their sets or play with a final moveslot to work around checks. But Chomp doesn't do this, and you've actually picked some pretty poor examples to support your point too. Chomp doesn't, on any set, pick out from an open moveslot to annoy things that would otherwise check it, in the same way that Clefable can choose between Flamethrower'ing steel switch ins or spreading paralysis, or that TG Manaphy can pick it's attacks based around breaking for it's teammates. Whereas Chomp just doesn't do this on any one of it's sets, but rather, takes a different set on entirely. If it needs to beat faster things, it has to change it's function entirely by running scarf or salac. If it wants to beat bulkier walls and balance cores, it has to set up SD. If it wants to have any chance of checking bird spam or volt-turn for very long, it usually has to be tank chomp. And, even then, most of those things will have a way around it.
Now, I can't call your examples and justifications poor without explaining myself, so, sorry, but here goes:
Keldeo, Latios and Mega-Man aren't all 'beaten' flat out by Sub Salac. Keldeo isn't even close to 1HKO'd -
252 Atk Garchomp Earthquake vs. 0 HP / 4 Def Keldeo: 178-210 (55.1 - 65%) -- guaranteed 2HKO - so even with some prior damage, you still need to be running scarf or already have your Salac up (and hope that Keldeo itself isn't scarf'd). Salac Chomp is very threatened by attacks from both of the other two too (draco/psyshock from Lati, HP Ice from Manectric. Plus, Chomp has to get the salac berry eaten before it can hope to win; anyone who sits there breaking subs against chomp is making a very bad play, especially when it's so easy to scout for that set with a knock off user capable of breaking sub. Not to mention, that set
does lose to Clefable, because without the life orb it can't easily 2HKO, and if you're trying to sub, it becomes a lot more difficult to read your opponents plays once they work out that you're trying to get a Salac off. Not to mention, you need to guarantee the kill after subbing yourself into Salac range, because Clef no longer needs to worry about damage calcs when firing a Moonblast at you. Neither of Latios and Mega Man are going to switch in on any chomp set, be it Salac or other, but both can force chomp out easily unless he's Scarfed, so, they're worthwhile mentions when considering Chomps matchup against offense, not 'kind of silly'.
TankChomps final slot is versatile, but one's kidding oneself if they think that he has everything he wants outside of that moveslot. The choice between Fire Blast, Toxic and Endure isn't exactly a 'yes look I get all these extra options' kind of choice, it's a 'right I need to choose between matching a bit more favourably against x and x'. And, in that regard, all Chomp beats with Fire Blast is (Mega) Scizor. And only non-bulky variants at that. Before people cry Skarm, here:
0- SpA Garchomp Fire Blast vs. 252 HP / 4 SpD Skarmory: 158-186 (47.3 - 55.6%) -- 21.5% chance to 2HKO after Leftovers recovery. And:
0- SpA Garchomp Fire Blast vs. 252 HP / 252+ SpD Skarmory: 108-128 (32.3 - 38.3%) -- 2.5% chance to 3HKO after Leftovers recovery. And the most common Ferro spread, too, for good measure:
0- SpA Garchomp Fire Blast vs. 252 HP / 168 SpD Ferrothorn: 180-216 (51.1 - 61.3%) -- 92.6% chance to 2HKO after Leftovers recovery.
Iron head isn't a viable thing. On any set. Period. (Nor is Iron Tail, really, it's not reliable and would exist solely for that purpose when any team should really have a solid answer to Clefable that isn't Garchomp too). What does it hit? So, it get's a 10 BP boost against Clef when compared to a STAB EQ... but EQ already 2HKO's Max Def Clef, as you stated. Again, SD choosing between Stone Edge and Sub (and Fire Fang/Blast, if you fancy) isn't an advantage in the way that you put it. Moreover, it's choosing between protection from the ever common WoW cripplers (at the cost of another turn of set up, no less), and getting a bigger hit on a few things that are already hit suitably hard with a Dragon Claw. I wouldn't exactly call Mandibuzz of all things relevant enough to influence an S-Rank decision, and Thundy/Torn/TF are all hit hard enough by Dragon Claw...
With regards to the 'no guaranteed counters' thing, I'd say your quite mistaken:
SpD Skarm:
0- SpA Garchomp Fire Blast vs. 252 HP / 252+ SpD Skarmory: 108-128 (32.3 - 38.3%) -- 2.5% chance to 3HKO after Leftovers recovery
Ferro, under rain:
0- SpA Garchomp Fire Blast vs. 252 HP / 252+ SpD Skarmory: 108-128 (32.3 - 38.3%) -- 2.5% chance to 3HKO after Leftovers recovery Say what you will about rain's own viability, it's a prime place to put Ferrothorn, and when preparing for rain, any team should be ready to see Ferrothorn, and, well, when under rain, Ferro beats Chomp easily. This doesn't even factor in Leech Seed or Protect turns.
Pretty standard Hippo:
252 Atk Life Orb Garchomp Earthquake vs. 252 HP / 144+ Def Hippowdon: 149-177 (35.4 - 42.1%) -- guaranteed 3HKO after Stealth Rock and Leftovers recovery, switches in on set up, and whirlwinds. Can't 1HKO even at +2
(Non LO: 252 Atk Garchomp Earthquake vs. 252 HP / 144+ Def Hippowdon: 115-136 (27.3 - 32.3%) -- 99.4% chance to 4HKO after Stealth Rock and Leftovers recovery)
SpD Klefki (with
Prankster Magnet Rise):
0- SpA Garchomp Fire Blast vs. 252 HP / 252+ SpD Klefki: 94-112 (29.5 - 35.2%) -- guaranteed 4HKO after Leftovers recovery
Slowbro:
252 Atk Garchomp Earthquake vs. 252 HP / 232+ Def Slowbro: 112-133 (28.4 - 33.7%) -- 0.9% chance to 3HKO after Stealth Rock and Leftovers recovery barely 2HKOs after an SD. Chomp takes close to 50% from a scald, so probably loses factoring in a turn to set up and LO/rocks damage.
Mega Venusaur:
0 SpA Mega Venusaur Giga Drain vs. 12 HP / 0 SpD Garchomp: 109-130 (30.2 - 36.1%) -- 48.9% chance to 3HKO. Again, relying on set up to even 2HKO, and thats not accounting for Leech Seed and Giga Drain.
Gliscor:
252 Atk Garchomp Dragon Claw vs. 252 HP / 56+ Def Gliscor: 94-112 (26.5 - 31.6%) -- possible 5HKO after Poison Heal Again, comes close to a guaranteed 2HKO with set up after poison heal, but that doesn't factor in protect/sub turns form Gliscor. Chomp just plain relies on set up.
All of these guaranteed counter at least one Garchomp set - you can't base an argument against a counter on bad plays, and letting Chomp get to +4 or +6 is definitely a bad play when you have one of these available. Most of the things I've just listed have reliable recovery too, and only come even close to losing to Chomp after set up which gives them a turn to either switch in, or just top themselves off if Chomp tries to set up in their faces. Most of them have an answer to Chomp themselves too; Bro nearly 2HKOs, Venusaur 3HKOs which means that Chomp can only win if he's magically at 100% on every matchup. Hippo can whirlwind out or take off roughly 35% with an EQ. Heck, if we're talking niche picks, Hippo can even run Ice Fang, although probably then runs a risk due to Rough Skin chip damage.
In that regard, I think a move up for Chomp now is even less timely than it would have been a few weeks ago; Hippo's rising in popularity in the current meta, which is a great stop to most Chomp sets, all of which rely on set up to beat it (if they even can at all). Klefki's as popular as it ever has been, but in the last few months people have clocked onto Magnet Rise, which means that all Chomp can really rely on to hit it at all hard is Fire Fang (in other words, Chomp can't function without a good answer to Klefki to support him). Not to mention the somewhat obvious rise in popularity of Weavile, who takes a minimum of 95% off of non-tankchomp sets with Ice Shard, and flat 1HKO's all chomps with Icicle Crash (i.e., long story short, the only situation that Chomp wins there is if it's at 100%, or Weavile tries to switch in). Heck, Mamoswine has the same properties when considering chomp, just with enough power to guarantee the 1HKO with Ice Shard against non-tank variants of chomp, and altho Mamo is a less common and less viable component of most teams these days, you can't say that Chomp should be any less prepared for it than Weavile.
Ultimately, the current metagame is very prepared for Garchomp (heck, I just named basically every go-to defensive choice in the current meta bar Clefable because you already covered that calc yourself), and while he can be very threatening, he's extremely reliant on multiple kinds of set up. And, each set is vulnerable to something different; once the opponent works out what set Chomp has, the cards are all on the table in that regard. Pick 6 random mons from A-, A or A+, and chances are you've got a way around him. He's a valid concern when team building, sure, but unlike the current S Rankers, if you build any sort of thought through team, chances are you've covered all of his sets somewhere without taking a dedicated 'I need x to beat x variant of Chomp' sort of decision.
I guess I think the most important question is: can we really pin down and justify the fact that Chomp is notably more threatening and viable a team choice than
everything else in A+? If not, he's probably not S. In my opinion, that's the exact case - he's another one of the definition A+ pokemon for me.
EDIT: Just realised my Klefki calc had rain on... hmm. Point still stands when Fire Blast is a 4HKO after lefties (3HKO with LO) :/