1. Magneto decides to take SHIELD down, he doesn't have to kill everybody in it, just destroy the organization's functionality. He gets a week of prep. Can he do it?
2. Shield sets up a manhunt for the most dangerous mutant on the planet and Magneto, aware that he is being hunted, decides he'll sink that helicarrier and the bureaucrats behind it in the bottom of the ocean before any damn dirty ape gets his paws on him. Both sides get a month of prep before they make their moves.
Apocalypse is the most dangerous mutant on earth BTW. The Eternals compared him to Mags and said that what Mags has done is nothing to immortal Apocalypse.
They did. They said something like "Magneto is just a mortal but you are an immortal" to Apocalypse. That's obviously not exactly what they said but I can assure you that they did.
Apocalypse is also more powerful than Magneto and has technopathy.
I would imagine that once Magneto strikes, SHIELD would mobilize the Avengers to deal with him or something else. It's certainly possible for him to do a sudden amount of crippling damage before SHIELD can respond fast enough and that's without prep. With prep, Magneto should be able to succeed.
Yes, of course he takes a dump over all the other Avengers. They're not in this fight though. Shield can mobilize any one who is actually a member of their ranks officially, but no simpathy from outer groups. Mags doesn't get to recruit an army of mutants either.