Yes, there are many slots already. A possibility would be to add a manual toggle on the clothing menu, dictating if a bottom clothing would go on top of below the top clothing (not coats, ofc) at the player's discretion. I doubt there would be a need for this on say... underwear (unless you're Superman and wear your underwear above your bodysuit
). If you find a way to make this look unobtrusive on the interface, it seems it would be a pretty harmless change.
Just my 2 cents though
. No clue what kind of other complications that might generate.