As a photographer I come at this from a different angle. How about presenting enough like your former female self to satisfy your mom (and the college) but make it easy for someone to photoshop you back to your male look? The gown color would be easy enough to change. If the collar is different, just make sure you get a good picture of one of the males so their gown can be "cloned" onto your picture. It's easy to add elements to a photo. A little harder to remove things.
Your "official" graduation photo would work for the traditionalist and you would have a Ze photo for your memories. Opting for the gown photos would avoid the problems associated with a skirt and blouse. Good luck and congratulations!
