I can't think of many other villains that applies to, I guess the Silence are connected to Eleven fundamentally for story arc purposes? I think even the Valeyard can be separated from Six's run but Sil just feels like the perfect foil you can't really take him out of the 80s.
Also I think RTD would get extremely weird about Sil if he was to return (was he gonna be the Boss?), like he'd be on Unleashed saying "we can't have a disabled Arab play a villain" meanwhile said disabled Arab would like "LEMMA PLAY THE VILLAIN GODDAMMIT DON'T TURN ME INTO A CGI SLUG"