Yeah they’re the same characters in a continuous story, but Ao3 treats it as separate fandoms.

My thing is that if they’re nominated under the newer installment a lot of folks won’t even look at requests for that because of spoilers. But if they’re nominated under the other, then you’re forced to put potential spoilers in with the older stuff if you want to request it. (It’s a JRPG series where the most recent installment isn’t localized)