I think I should be in the clear. All I've done to my trainer is change his skin tone, but I never Game Synced until after the fact. I've synced twice and still no ban, but I'm crossing my fingers it stays that way. On my previous playthrough, I did give myself max rainbow beans and got all the Pelago islands that way .. not sure if that would've been grounds for a ban or not, but definitely trying to play this playthrough without using PKHeX as much, only hacking in things that'd make the game more fun and less of a grind (6IV Dittos for breeding, for example).
But yeah, it's becoming more and more clear that these bans are happening from carelessly hacking in things that aren't possible, like shiny-locked legendaries, complete Pokédex entries before Bank, getting Marshadow, trainer modifications, etc. It never mattered before, but apparently it is now. Maybe that'll lessen the chances of getting pitted against a ridiculously hacked team in rating battles.