Imber doesn't actually pilot IS, he pilot a machine which he programmed to function similar to IS.
Cipher use Prototype IS core which is developed by male and female which has no gender restriction.
Out of the three, Alex is true IS pilot. There is no explanation for why he can pilot IS other than the fact that he looked so much like a girl that even the IS is confused by his real gender.
Edit:
Due to the Dubious nature of Imber's and Cipher's machine, they are grouped together in the same class while Alex is assigned to same class as Ichika.
Moar Edit: It doesn't really matter that much since the story isn't serious in the first place.