I have no issue with Magneto joining the X-Men at this juncture since they are following his ideas more than Xavier's, but...
A. As (sort of noted) by the OP, Magneto's helmet has never blocked telepathy in the 616. That's the films and the Ultimate Universe. (And if people want examples, I can cite many, many issues.)
B. Magneto's bitchy dismissal of Charles. How did we go from Legacy to this?
C. Magneto bows to/lay his sword at the feet of no one. If Magneto was approaching Cyclops as an equal that would be stretching it, but at least within the bounds of possibility. It just isn't in Magneto to be subservient. Fraction is just warping another character to build up his man-crush Scott. He can't actually show that Scott is a good leader (since Cyclops has been making remarkably stupid decisions lately), so he has to have everyone standing around *saying* Cyclops is a good leader.
The other option is Fraction is making this a "wolf in sheep's clothing" ruse and Magneto will turn on them in a particularly villainous manner...so that Cyclops looks good by comparison and he can get every to shut up about how Cyclops is cribbing from Magneto's playbook.