I'm pretty sure Doom's armour has a specific failsafe against Magneto's electromagnetism (although it may not be automatic?), however I don't think he's protected from mutant powers as a whole.
Not sure who wins in a non-prep fight. Sinister's control of his structure makes him damn near impossible to kill, he's also a telepath and telekinetic with (low level but higher than Doom's) superhuman strength. He may not be on intellectual par with Doom, because no one is 😂 but he is a genius in his own right.