However, have you ever had those moments where a Pokemon can just sit on T-Wave Chansey and heal off Seismic Toss damage?
Oh, for sure! It's a situation that happens fairly often, I've found that the best scenario there is just to go into something else. If you've got the target paralysed, then you're reasonably okay to swap into something that can handle it, especially if you can predict their heal, which gives you an opportunity to swap. It's very much a personal choice, as you say, but my play- and teambuilding style tends to revolve around waiting for the perfect opportunity to go for a setup, for example with something like Magearna or Calm Mind Lele (which I find to work especially well with this, owing to the fact it outspeeds enough paralysed mons to go for a +1 or +2 sweep, and loves Gliscor dealing with stuff like Heatran). Toxic is absolutely usable here, for sure. Personal preference and team context moment. If you've already got a fast cleaner like (as an example) something with a Scarf, you'd probably prefer to have Toxic anyways (though I think this core sucks so much momentum it wants to be on a bulkier team). Regardless, I've gone ahead and edited the
importable to include Toxic Chansey, as it's very valid as an option over Thunder Wave.
And it is a threat, for so, so long (except when using the best mega in the tier

)
I don't disagree with you for sure, Latias is exceptionally consistent (and ironically enough works well with this core, almost turning it into a semi-stall team if you add Toxic Spikes Toxapex; though it's very consistently answered by Celesteela if paralysed, and Fairium Z Magearna (which is something that I very much like) if not:
224+ SpA Magearna Twinkle Tackle (195 BP) vs. +1 248 HP / 0 SpD Latias-Mega: 320-380 (88.1 - 104.6%) --
guaranteed OHKO after Stealth Rock
+1 0 SpA Latias-Mega Stored Power (60 BP) vs. 248 HP / 8 SpD Magearna: 57-68 (15.7 - 18.7%) --
guaranteed 6HKO after Stealth Rock
This pair of calcs assumes that you've switched Magearna in as Latias clicks Calm Mind (which seems to happen a fair amount), and just go straight for the Z-Move. If you've bought Magearna in at all, it's probably towards the end of the game so you can go for a countersweep of your own. If, however, you end up in a straight boosting war against Latias, then it looks like this:
+6 0 SpA Latias-Mega Stored Power (260 BP) vs. +4 248 HP / 8 SpD Magearna: 219-258 (60.3 - 71%) --
guaranteed 2HKO after Stealth Rock
Magearna tanks the Stored Power to retaliate with
+4 224+ SpA Magearna Twinkle Tackle (195 BP) vs. +6 248 HP / 0 SpD Latias-Mega: 362-428 (99.7 - 117.9%) --
guaranteed OHKO after Stealth Rock
The reason that Magearna is only at +4 in both of these examples is that you'll always be one turn behind Latias if you switch in, and you'll lose another turn to click Twinkle Tackle as Latias boosts to +6. Even if you're a turn late, I find Latias can always be handled by Magearna (unless it's Reflect Type, but Reflect Type Latias is exceptionally niche and not particularly consistent, I find). The Calm Mind + Pain Split set is the one I find myself most often running, but Shift Gear + Calm Mind with Fairium Z Fleur Cannon and Focus Blast is most definitely an option if you want to get the drop on a lot of pokemon like Scarf Landorus (immune to Thunder Wave) or Scarf Kartana (immune to Toxic and threatens Chansey out with Sacred Sword).
Tornadus also likes to run Supersonic Skystrike if you prefer over the bulkier Helmet set, just to guarantee that it can beat Normalium Z Kartana - relying on a 75% accurate Hurricane to KO something that will singlehandedly rip through a team if it can get to +2 and click Z-Giga Impact vs the bird really isn't a strategy. SSSS is a much more consistent answer, the only problem being that Magearna / Lele really want to be running the Z-Move. It does, however, provide you with this especially funny calc vs the really annoying thing with the Rocky Helmet that likes to switch in vs it, for some reason, predicting the U-Turn:
252 SpA Tornadus-Therian Supersonic Skystrike (185 BP) vs. 252 HP / 0 SpD Landorus-Therian: 322-381 (84.2 - 99.7%) --
75% chance to OHKO after Stealth Rock
I do, though, usually run Rocky Helmet. It's another interesting choice for Flyinium Z, but again, you really want the bulk.
Rain is mid+ mu fish but getting yourself a water resist can't hurt as a team partner.
Rain matchup is manageable, as you say, but I often find that you end up having to sack something in order to click a move, especially vs Swampert-M. Again, one of those situations where Toxic > Thunder Wave. Suggestions for that would be hugely appreciated. Maybe Scarf Serperior for Glare?
I've also linked two nearly-complete teams where I've built around the defensive synergy of Chansey + Gliscor, both using Rocky Helmet Tornadus-T and a variant of a Calm Mind setup sweeper (the Magearna team is probably much better tbh, but it's just too slow. Shift Gear might be a better option), plus Celesteela, which I personally prefer over Skarmory just for the better MU into opposing Lele.
Team 1: CM + Pain Split Magearna
Team 2: CM + Fightinium Z Tapu Lele
Again, critiques on both of these (but primarily the first one considering it's the one I've been using the most) would be much appreciated :)