While waiting for Hakchi2 for SNES I solved the problem of the annoying face cover... I know its locking pins will break someday so!
I inserted my 8bitdo retro receiver inside a clone of controller port 1 which is inside the console itself.
Pretty easy to do if you have a retro receiver for NES/SNES classic
see attach pictures!!
So you still have the original ports but added an extra one inside?