Well, there are some circumstances in their last fight we shouldn't forget about.
1) Proteus demonstrated the powers necessary to kill Magneto
2) Proteus never had the intention of killing him outright, but to wear him down and posess him
3) Magneto didn't resist the reality warping per se, just posession
So, in this fight Kevin turns his blood in cyanide instead of lead.
That being said, since Mags now knows how his energy is composed, he may be able to disperse Proteus with a single attack... Although, it may not work with Kevin expecting that.
Protheus is too stupid for this fight, he is a reality warping rhino.
But with CIS off, he could oneshot magneto into nerf.
Magneto's best bet is that he now knows how to control proteus energy matrix and explode it.
Could go either way, depending on who makes the first move. Although Magneto probably requires more concentration, specially the current version, than the instantaneous attacks proteus usualy delivers.
Well, Magneto has the faster reaction time. Since Magneto can manipulate psionic energy, defeating Proteus will not pose a major problem and Proteus can't warp reality is his own psionic energy is being manipulated.