I think this is an excellent question, considering the...errr....unique feature of FED football that allows more than one forward pass.
The only place I could find a mention of a passer losing the "special protection" of the roughing penalty is on a play where he is beyond the neutral zone. I would say that if it is a legal passing play then it is roughing.
Of course, don't forget the flag for the ineligible downfield.
Rich