I find when young children come to this web site, they will talk to me, a total stranger and not their parents. This is because they have a strong emotional attachments to their parents where as I am a stranger they can talk freely to without risk. The therapist is currently filling the role I would. At some point, your child will get his issues resolved to the point where he can talk to you without the fear we all have or had with our parents.
For now let the therapist do the work and ask the therapist what you can do to help.
As for not knowing how how your child felt, I hid my feeling from my parents between age 13 and 23. We are pretty rare at about 1 in 600 births and there isn't any reason to have parents know all about us when the odds are they may never know or meet one of us in their life. Some people do know something is wrong at age 3 or 4 and while I didn't exactly live a normal childhood when I was young, I didn't figure it out until age 13. A few discover what they are much latter in life.
I had a pretty normal male upbringing but I was the nerd type. I wasn't interested in sports or normal male play but thanks to my dad, I learned to work with my hands doing wood work, electronics, science, photography, auto repair and general repairs of most anything I could get my hands on. In college, I picked up my profession of computer programming. Much of this time I was struggling with my identity. These activities helped keep my brain busy so I didn't spend all my time thinking about my problems.
We have something called the sexual spectrum. That means there are two extremes where normal people are on one end and transexuals like me are on the other end. Exactly where your child is in the spectrum is unclear at the moment. That is one of the things the therapist is helping your child explore.
You are being a very good parent because you have your child in therapy, and you want to help however you can. You also took the extra step to come here in order to learn more. Not all parents do this but you are doing all you can at the moment. Your time to help will come latter.
If I can help you, post your questions to this thread and I will respond when I see your post. Also feel free to ask me any personal questions you might have. I am comfortable with my past and welcome questions about it.