It really doesn't matter if he is putting on makeup or lipgloss or perfume. And if you're going to get on his case about toning down perfume, you'll have to make sure you get on all the other kids too, as ALL jr. high kids wear WAY too much perfume and cologne. :) As to sexual behaviors: these days ALL sexual behavior is risky, whether it be heterosexual or homosexual. So I don't think it's appropriate to single him out to 'preach' about the risks of a 'homosexual' lifestyle.
The kid is attention seeking. However, it's not worth making a big deal over. If he's a frequent flier in the nurse's office, then the issue needs to be addressed. I'm willing to bet his peers are less than supportive of his oddness, and he's having issues with the other kids. Maybe he sees you as a safe person and your office as a safe place. The school counselor should also be aware of him, if that person is not already. I think you are bothered by a boy acting like a girl. That's ok, but you need to make sure that feeling doesn't interfere with your care of this kid or any other kid like him.
For the record, I've seen girls who pretend to be boys, as well as boys trying to look like girls. Some of these kids will 'grow' out of their particular way of creating shock value in the adults around them, but a lot of them will not and will struggle for the rest of their lives with their sexual identities. There is a high suicide rate among gay/transgendered kids.