Apocalypse does not have reality warping powers. I don't know where you get that impression. Magneto can overpower Apocalypse's own molecular control by drawing energy and power from Earth's magnetic field. Magneto did this to Gideon in AOA.
Kitty Pryde can also go intangible. In Uncanny #150, Magneto zapped Kitty with electricity when she tried to pass through him and he nearly killed her. As long as it can conduct electricity, it's vulnerable to him. Magneto can manipulate Apocalypse's malleable form rather easily.
You can think whatever you want, but I have comics and science to back up my side of the argument. Electromagnetism is the force that holds all matter together. It is one of the most prevalent forces in Physics. Any form of technology that Apocalypse throws at Magneto, Magneto has control over.
Without outside assistance, Apocalypse cannot defeat Magneto. Part of Apocalypse's molecular make up is nano-technology based. Magneto controls electromagnetism, which means he has absolute control of the material Apocalypse is made out of and the energy it runs on. Apocalypse is a sitting duck. Apocalypse also has the techno-organic virus, which makes him vulnerable to Magneto as well.
Magneto also has access to extremely advanced technology that is a combination of all the alien races that he has encountered.