The ONLY problem I have had with this, is the controller on the system itself defaults as controller 1, so SOME games it takes a little fiddling to use different controllers. But I have done this and it works great.

I don't know if you're talking about in-game fiddling or Steam Input but to clarify for others here: Steam allows to reorder the controllers, so the thing I usually do at the beginning of game party is to move the Deck's integrated inputs to the last place.