I think Bendis just didn't want that fourth Beast around to screw things up for the two he introduced.
I don't know where we've landed on the powers thing but I'm guessing this does not mean their powers are fixed. Why would the nanobots give cyclops a power up as well as screw with his control? Magik didn't wind up in custody, I don't think her power up at the same time is a coincidence. I think it's just referring to their recent malfunctions.