In a perfect world...
This is my fear for the OP. Or that worse, he says the OP tried to coerce him into sex or something similar. Never underestimate someone when "cornered" if they feel there is no face-saving way out.
@AlexTrainer92 : Bottom line is that this young man needs to learn/understand that it's NEVER okay to rifle through/pilfer someone else's property. That's at best attempted theft.
And if he doesn't learn that soon, what's to prevent him from doing it to another guy/student who may not react as the OP did. I would hate that young man to be on the receiving end of a beat down for such behavior by someone who doesn't know him like the OP does and realize he may be struggling with his sexuality. Not many other people would be as understanding as you have been.
Right now, IMO, the best bet would be to let this go; you both know what went down when you confronted him in the act.
What might be beneficial is at the appropriate time/circumstance to let him know if he ever wants to talk, about anything, you are there for him. Confidential and no judgement. You could also offer him the links to/information about where he can purchase his own under clothing.
Good luck and I hope this young man figures out who and what he is!