"If you're a minority, you have to file another form to get affirmative action.  That's where they'll scrutinize the 'boxes' more closely."

 That's pretty much what I am thinking.  This is one application at one college and I don't see anything about that application having influence elsewhere.

 That application doesn't change anything about how that individual is interpreted by the people around them as far as I can tell, but its new so we don't know what the effects might be.  I don't think it will change how people analyze one's gender or race.

 I am under the impression that the "girl" box for "identify as" is personal.  

 Everyone else will see a man, your gender is male biologically, you are a male student, can participate in male sports, can be in male fraternities.  You can not be in female dorms, be in sororities, apply for female scholarships or play female sports.

 Is the college saying they will categorize applicants based off of chosen identity?  You identify as female and can bunk in a female dorm?