>>56536070I think letting you pick whoever in Rescue Team was the original intent, as the game still has partner-only portraits and animations programmed in. (pic related is an example) My guess is that they decided to lock the partner selection after playtesters got stuck or something, as certain combinations would make the game pretty difficult. (this is probably also why they decided to give the extra starters in Sky 1 egg move each)
You can use a code to force the partner and all this stuff will work, unfortunately they do lack the few lines of in-dungeon dialogue.