Its been a long time since i read the comic, so sorry if the details are a little off
From what I can tell, magneto's powers are about the same in the Age of Apocalypse....Apocalypse himself seems stronger than his real world counterpart.
Okay, the only occurance of this Fight i have read was at the very end of the Age of apocalypse...it is in the final issue of X-Men Age of Apocalypse called Omega (its a foil back cover, with amazing art)...One of my fav comics...From what I remember, its a pretty much 1on1 fair fight, in the end...though I think Magneto had been beat down a bit before the fight...Magneto had nothing but his helmet, because he had been held captive by apocalypse...he was just wearing a skin tight black suit and his helmet....But mid fight, they fight into a Junk yard, full of Red metal, where magneto constructs himself a suit out of the metal (that BTW, looks totally rad). Anyways, magneto gets beat, and BAD for a long time, blood and cuts all over him...but in the end of the fight Apocalypse is like "WHY AREN'T YOU FIGHTING BACK?" and magneto is like "I Can't..." and Apocalypse calls him a coward and stuff, and Magneto is like "I can't, im concentrating..."..and apocalypse is like..."what?" and magneto Uses an energy attack, essentially tearing apocalypse's body completley in half...He was letting himself get beat down so he could focus on one HUGE attack...it was awesome