NTA.

Not by a far stretch of the mind. I can't believe the amount or moronic comments we have here. That's why you shouldn't ask for advice or opinions online.

You're perfectly right. If your son wears a skirt at school he will get DESTROYED. Bullied to no end and suffer the consequences of being different. That's the real world. Not the bullshit I've been reading in the comments with a bunch of self-righteous peeps trying to have you believe that you're in the wrong here.

You said very clearly that you're are fine with him dressing however he likes when he's not at school. Yet, the dummy brigade is ignoring this and playing the 'I've been a LGBT supporter my whole life, oohhhh how can you do this to your son?! Do you even love him?!!' F them.

What I would do :

Have a very serious sit down with him. Once again explaining how much suffering he's about to face and... allow him to dress exactly the way he wants. You have play the reverse psychology card here. He's a teenager. If your parents forbid you to do something, you'll want to do it even more, you already know that. If you completely allow him to do it and say something like 'Ok, fine. I'll make sure we've got band-aids and icepacks in stock. I'll be here for you if you need me but don't tell me that I haven't warned you when shit hits the fan because it will.'

Then wait.

If you're very lucky. Nothing ever happens because the entire school is extra progressive (hahah...right...). If you're unlucky, he takes a beating and stops it on his own.

Regardless. Don't take his clothes away. That's a very bad move.

I fully understand where you're coming from and how painful this must be.