This is a bit of an abstract concept, so I'll try to explain it as best as I can. The issue with any high-ranked threat isn't that a small group of otherwise unviable mons become viable because of it. Lanturn is considered viable for stopping every Volt Switcher in the meta, but no one is calling for Volt Switch to be banned. The issue is usually the necessity of running these otherwise niche mons. Back when Mega Mawile was in the meta, the number of things that could safely stop it were close to 0, and while there were some non-niche solutions, there were very few, which is why Arcanine was ever ranked: he was one of the very few non-Mega solutions to Mega Mawile. However, was only considered viable until Mega Mawile was banned, and was immediately unranked after that. Conversely, the Volt Switchers in the meta have plenty of good checks beyond just Lanturn, so since no one is really forced to rely on it, no one really cares to do anything about Volt Switch.Abc encompasses all Pokemon not considered viable, and last time I checked, Smogon as a whole dues not care about making Pokemon more viable but they care about the meta game as a whole. Greninja seems to be only causing the problem that people are running Pokemon that they don't like, from group xyz, when they want the meta to allow usage and viability for certain, not necessarily specific, Pokemon in group abc, but seeing as Smogon has already said we don't Carter to such whims I have a hard time understanding why this concept, referred to as centralization, is bad for the meta game.
Now, Greninja is a different story. Everything listed that checks Greninja is at least C rank on the viability thread, thus we can't claim that Greninja is forcing us to use mons that are otherwise unviable since there's no way they'd be ranked C for ONLY checking Greninja. The issue is the nature of the checks themselves. For the most part, the checks are either blazing fast and frail or very passive but sturdy. When building a balanced team, it's important that your defensive core have some form of offensive presence so your core isn't set-up fodder, and it's important that your offensive core have at least one or two members who can switch in on resisted hits once your defensive core creates a switch opportunity. If you look at what can check Greninja, very few mons fall under these criteria; the defensive checks are very passive, and the offensive threats have issues switching in even on resisted hits. There are few things that check Greninja AND fit the criteria, and most are Megas. This is what is causing the decay of balance: not the use of bad mons, but mons that just don't work with the playstyle. Now, could a balance team be formed that works in a Greninja meta? Probably. Will they have any real diversity to them? Not likely.
Black listing tends to come from less from a Pokemon being bad but the toxic discussion from it or constant repeated arguments. Jolteon was blacklisted because its ONLY niche was killing Greninja, and yet it was brought up like 4 times with no new insight other than "it kills Greninja". Darmanitan was blacklisted not just for being outclassed, but the guy who brought it up argued for pages by bringing up the same points repeatedly while ignoring every counterargument brought up.Unfortunately, that is the case and some Pokemon are even blacklisted from discussion because of how unviable they are.
Prime example is Volt Switch Toxic Orb Jolteon who, when supported properly, annihilated Greninja because he out speeds most scarfers. But we're not allowed to talk about him so we won't.