Since Pokemon Tabletop United seems to be an unofficial fan created system, characters from it fall under the We do not permit original characters from closed canons rule. You would thus have to rewrite the preincarnation backstory to not include Pokemon at all, and treat the characters as full OCs for app purposes (aka you would have to briefly outline the world they live in as part of your canon history).

Instead of omitting the pokemon completely, you could also file off the serial numbers and keep "legendary animals with special powers", or something to that end, as long as they are not recognizable as pokemon anymore. Any other canon elements (characters, setting details) would also have to be unrecognizable for characters from Pokemon canon.

It's up to the player if combo characters share an account or not! All they have to share is an info post.