In the case of Soren Tucker, it's an issue of legality and procrastination (on the part of the "victim"), and not transphobia. If the student wants to be identified as "Soren" during the graduation ceremony, they should change their legal name accordingly.

A lack of action on Soren's part does not constitute transphobia on the school's part. (If either of Soren's parents are blocking a legal name change, then it's a whole other issue, but still not the fault of the school.)