You're right in that when the statistics are analyzed, there must be
some factor differentiating Sm4sh Bayonetta from Brawl MK and Melee Fox, but who says it has to be community stigma? That argument underestimates the ability of people to change their character, and also the
willingness of people to change their character. Bayonetta came in the last DLC pack, pretty far into Sm4sh's lifespan. Everyone who was good enough to be a competitive player, whether they be a top 10 veteran or just some local monster/wifi warrior (i.e. Bayo mains before the character was released) already had some character, typically another top tier with a strong capability to win, who they already liked and had sunken hundreds if not thousands of hours into. The idea that some 40% of the playerbase is going to abandon the top tiers they already know how to use for another character when that character is entering the game 2 years late and when most of their playstyles and favorites are completely, irreconciliably different is unreasonable to imagine. I think the way a disproportionate amount of Bayo players used to play Peach is already evidence of a playstyle factor being involved. The fact that she is DLC matters a lot.
Not only that, but I think it is dishonest to say that there wasn't some grand stigma around Meta Knight in Brawl. I want a Brawl vet to chime in on this as verification, but I'm fairly sure the things people said about MK online and even in-person were just as bad if not worse than the stuff people said about Bayonetta more recently. Look at the YouTube comments on Meta Knight VODs from 10 years ago. Listen to the stories. If we're calling the way people treated Bayonetta a stigma affecting character choice, than why wouldn't Meta Knight go the same way?
Also, nitpick: There was a top 100 ranking at the end of Brawl's life with equivalent prestige and accuracy. (
https://www.ssbwiki.com/2014_SSBBRank) your stats were about the same, though: approx. 40% of the list has Meta Knight in it.