I think maybe a case-by-case basis would work best. For example, Fate/Grand Order is relatively in-continuity with the rest of Fateverse, though it can stand alone for those new to the series -- it still assumes that the Servants have knowledge of their other appearances, and so on. Tales of Asteria, on the other hand, is a crossover that goes whole-hog AU with its Tales characters. I haven't played Dissidia and didn't get too far with the story in KHUX, so the above two are the cases I'm more familiar with.

Either way, I believe the game only allows one version of a character at any given time, so if a Tales character were apped from one of the mobage counterparts, they wouldn't be able to be apped from their original game, and vice versa. In that case, it might make sense and be simpler to just count them as part of the cast cap for their original game since no other version can be in-game anyway.

Mobage-original characters for crossover mobages, though, are also a thing. In those cases I'd advocate considering them part of the cast cap for the mobage canon.

It definitely gets pretty complicated once you get into these, so ultimately it comes down to whatever is easiest to process for the mods.