It wouldn't matter anyways since Captain Atom can potentially manipulate the entire unifield which something Magneto wouldn't acheive. Hell, back before Wildstorm he was creating gravity wells to suck cities in.
The Ray also has electro-magnetic powers, but that didn't stop Nate for shutting him down. What can Magneto do to him since his skin would most likely absorb magnetic energy, through sub-marines at him? CA casually blew up large ships in the past.
Lastly he defeated Dr Diehard with ease, a slightly less powerful clone of Magneto. The same guy that owned Metamorpho via polarizing the air when Rex was in gas form and knocked him out.