Hi Jen,
First, I think it's great that you want to help out your student. If he's not totally out, you're probably doing all that you can do for him. Continue to point him toward community resources, support groups, etc. I would definitely encourage him to take advantage of the free college if his parents are paying for it. I know it seems awful to continue to delay transition once you're 18, but for most FTMs there's really no harm in waiting as long as you can mentally handle it. And he'd just be in such a better place with a degree and no student loan debt. He could hypothetically get a job during college and save all that money in a transition fund for once he's no longer under mom and dad's thumb. That is what I would recommend!
Again - I think it's great that you're being supportive and helping him. Everyone should be so lucky to have someone who cares about them!