If we got a Golden Sun character and it’s not Isaac, I’d take that as near-confirmation of “already had an AT” being a rule, personally; Felix may be the main character of the second game, but there’s no reason to not have Isaac when he’s in all 3 games, important in at least two of them (being the father of Matthew in the third game; still haven’t gotten to actually playing the games beyond the start, so still not fully aware of stuff, but I think Isaac would be cool), and he can do what the other main characters do.
I guess it’d still make some sense for them to have another character, but it’s not like P/M and Rex seeming to be just as important as each other in one game along with ARMS having no main character (as there’s no story mode though Spring Man is clearly pushed more and is the hero, but the creator wanted Min Min and there’s still no main character ingame I guess beyond Spring Man having his own metal clone), so not choosing Isaac would just be weird. If the “no AT” thing is a rule, though, it’d still be weird imo because it feels like “why does it matter? You have Mario beating up 7 other Marios, you can disable ATs sometimes for seemingly no reason on certain stages and likely could tie their availability to chosen characters, you gave Bomberman a DLC mii costume that looks identical to his AT...very dumb, man.”
Due to what I described, I really just believe ATs themselves don’t disconfirm and it’s up to other factors, but I would start to believe it more if they really went with someone over Isaac. I would just hope Sakurai and Nintendo actually flat-out say it at that moment; they have no problem disconfirming other characters due to their circumstances, why not disconfirm ATs etc. getting potential upgrades through DLC if y’all really care about that? Not to mention FP2 definitely not being planned out when ATs were made, so y’all could add them in as fighters now with a second chance - unless there’s reasons for not choosing them that have nothing to do with the fact they have an AT, which is far more reasonable, more believable, and better to argue in my personal opinion, but despite all this, it’d still feel like they’d have that dumb “no ATs” rule if they decided to look over Isaac instead of just replacing his AT, or giving it an alt. color/disabling it when he’s chosen.