it's not just reproductive organs though. my kid was at a school where there were two other kids who had very ambiguous appearances. in one situation a young white boy's parents let their son grow out his hair very long, to the point he looked like a girl. it confused my kid because they associated long hair with girls, but they also know that girls use a different bathroom than boys. so she noticed the difference and hit me with that 'why do they let that girl go to the boy's bathroom?'
in the other case there was a black girl whose lgbt parents always kept their daughter's hair cut short and always sent her to school in jeans and a t shirt. never any girly clothing. again, my kid hit with how is she a girl if she looks like a boy and dresses like a boy.
these are very difficult discussions to have with a child, because their comprehension skills aren't very developed. you also don't want to confuse them with gender ambiguous explanations. but you also have to keep in mind whatever you say to them will likely be spread around the class to the other kids. so i first addressed the question by stating how most girls and boys look and dress. then ended it with you can tell who is a girl or a boy by who the teacher lets go to the girl or boys bathroom...but not everyone is the same and sometimes you can't tell by the way they dress or their hair. i wasn't completely satisfied with my answer, but i knew i would have more opportunity to explain further down the line.
the one thing i can say is being a parent is the most difficult responsibility in the world. i can't imagine the challenges and the internal struggles lgbt parents have to deal with when their kids start asking them similar questions.
....
And therefore, he wants to wear girl stuff. 
He could very well, "like girls" or not like anyone at all, but just feel like a girl on the in/outside. A bunch of fukkery in my personal opinion, but that may be the case for him. 