Wiat a minute. You said Thanos has complete control over his molecular structure? How does this protect him from Magneto? 'cause, if it does, then Apocalypse should never have lost to Magneto because he has the same ability.
Without prep, they all lose. Neither Mags or Charles have teamed with Apocalypse before and they probably wouldn't be a good team without some prep. I say Apocalypse is smart and leaves the other two, deciding that survival of the fittest means he must survive by fleeing and living to fight another day. If he has to stay and fight, he'll die but be impressive. This is non-jobber Apocalypse who went toe-to-toe with the H.E. and the Prime Eternal. He will do well but I still think he's too smart to throw away his life in something like this.