It solves the problem if all the washrooms are gender neutral - otherwise it's no different than telling the student that they have to use the staff washroom or the one in the nurse's office.  A special washroom for transgendered students still singles them out.  Not only does it segregate them from their peers but it "outs them" to the rest of the school - it's quite possible that the fact that the student in question is transgendered is not common knowledge.