OP, I understand where you are coming from when you say this is a rubbish situation. I also have a little boy who likes what he likes and doesn't care if it's "supposed" to be for one gender or the other. I think that's wonderful and as it ideally should be. I have found some of the posts on here a bit overly fearful of the idea of boys not adhering to gender norms.
My son is a very friendly, inclusive person and has as many girls among his friends as boys. He doesn't want to be a girl but he will wear pink, rainbows and sequins when he wants to. Where we live loads of boys wear pink and no one seems to care.
I don't think it's ideal that school uniform is so gendered and it's annoying to have to make such a distinction between small girls and boys. My son feels it's not fair that he has fewer options for school clothes than the girls and that his options are more boring. I wouldn't personally have any objection to him wearing a skirt or summer dress to school if he wanted to but, as discussed in this thread, I also wouldn't want kids to make negative comments to him and I don't know of any other boys at his school doing so, so I would feel torn if he asked to.
I told him when he was younger that clothes are just clothes and there's no real reason why any colours or styles should be for girls or for boys. However, at a later point I did add that he may have noticed that most men and boys don't wear skirts, even though there's no good reason why - but they usually don't.
He has decided that he won't wear a skirt or dress to school because the other boys don't. He says he wishes people would wear whatever they like and I agree. He does wear pretty much whatever he wants out of school.
Good luck with your son and talking to him about the uniform. It's great that you are there to be positive about him exploring what he likes, but also sensitive to looking out for him. You sound like you are doing a great job. You'll find a way to navigate this that doesn't let it have too much weight, I bet.