In Silence of the Lambs, they tell you outright he's the one "bad guy" that shouldn't be dealt with, even while he's in a cage. So, yes, even though Bill was the main character Starling was after, it was made wholly apparent that Lecter was above them all. Bill was the "main antagonist", only due to the nature of Starling's job. Lecter was her personal antagonist, and by the end of the film, every single law enforcement agency in the states. You could swap Buffalo Bill with some random ass serial killer and it wouldn't matter in the slightest. It doesn't matter that Lecter was "helping" her or not: he's still an evil fukk.
This is also discounting the fact that he's in other films eating people and feeding people to themselves.
Same shyt with Magneto. Breh was in Days of Future Past helping, only because he had no choice. Everyone died in the future. You've got a whole trilogy where he was about to kill off every non-mutant person on Earth (a.k.a. committing genocide).
Bill's sub-bosses in Kill Bill Vol 1-2, might not have been the main villains, but they sure as hell were in that church killing and beating the fukk out of those random innocent people, for no reason other than Bill being pissy and simpin over Queen B.
Most of the villains posted are actual villains. I think the love for anti-heroes and romanticizing of certain films like Scarface, are causing some character details to get overlooked.