For those instances where you have two layered walls (for whatever reason - a small area of ceramic tile or furring that’s easier to manage as a layered wall) and need to have a door cut through both, I found this little gem on RevitCity:

You can use the ‘join geometry’ command to join the tile wall to the base wall and all openings will cut through both walls.

You should check for unintended consequences as always, but it seems to work well in my testing! Thanks to the Reviteer for posting this handy little tip.