It's hard to tell what you're asking about. This guy definitely seems to be into you. Those signs seem pretty unambiguous to me. Honestly, all you really have to do is send some signals back that his advances (and yes, I think that's what they are) are welcome. Maybe touch him back a little when he touches you in ways that you like. Maybe put your hand on top of his when he puts it on your leg, or if he comes up behind you and puts his arms around your waist, grab his wrists and pull his arms tighter around you. Things like that.
But you're also pointing out that you identify as a boy and are considering the possibility of someday transitioning, right? So are you also curious about how that might affect things if you start dating this guy more seriously? I assume he's straight, though it's possible he's bi. Obviously, transitioning may affect the relationship. As you get older and hopefully see a therapist about your feelings and how you identify, and if you decide to transition in some manner, I suspect you'll choose being true to yourself first regardless of how it affects your relationships, but that all depends on you. It's all very personal and something you should talk about with a therapist at some point.