Basically it does not seem to do anything noticeable (well, the legendary bonus seem to stack) and kind of solves itself with relog and stuff, so just enjoy:
Edit: Got to prev to test out. So basically when you go into your new loadout, it does not properly unsummon your old companion, so you can unsummon and summon your "actual" companion, but the one in your other loadout can't be unsummoned. It stacks up to any number you like and seems to only happen when you bought the loadout newly.