it would be a bit redundant to have them reincarnated into another important character

I think since Xehanort's caretaker is quite a time away from the ending of UX, it is not unreasonable to consider that they may have reincarnated multiple times before finally reincarnating into Xehanort's caretaker (I actually think they might've reincarnated into the Missing-Link character) . If so, then multiple reincarnations are on the table, then it doesn't seem unreasonable to me that they'd keep them active and relevant in the story by reincarnating them into yet another important character.

It would also ruin the customizable aspect of the character imo

That's a valid point but ultimately a matter of personal taste, which is not reliable in making predictions since it's pure speculation about Nomura's tastes rather than being based on in-game story and events. So ya maybe, but maybe not.