I think where it's ambiguous, it should be left to the parents to decide. Parents can already decline life-saving treatment on their child in the US due to their moral beliefs. Why not let parents also decide if they want to let a 16 yo have hormone treatments. It surely can't be more serious than declining blood transfusion.
This is, of course, the voice of sanity. Unfortunately it's not encoded into our legal system in these terms. On the other hand, if your religion explicitly requires that everyone "art theretofore honest with thy sentiment of masculinity or womanhood" (dress it up in colorful language, ideally quoted from old books with ambiguous authorship) you might have something you can sell to the Supreme Court.
I agree with your assessment, and I am suspicious of anyone (on either side) who claims that there is an obvious “correct” answer to this issue.