As for the first question- fandom OCs are a-ok! If there are any canon pokemon characters (such as Professor Willow who is an NPC in Kaisou) -- they will be treated as AU from one another.

As for the father figure/employee, you're allowed to have them be her adopted father in the AU. However they would be strictly an NPC status like any other AU family member where people can briefly interact with them and have handwaved relationships -- but there shouldn't be extensive threads starring the father since your main focus should be the character you app.

I hope this clears things up!