I think you may be over thinking this a bit. I'm sure you've been hit on by guys that you thought were cool but weren't attracted to before. How did you respond? Something along the lines of "I'd like to hang out with you, but I'm not interested in more than friends" right? Try that.
What his body may or may not look like in the future is a) no guarantee that you will then be attracted to him and b) not really your business at this point.
If he asks why, you say "I'm just not attracted to you." If he asks if it's because he's trans, you say, truthfully, "no." Though really, I doubt he'd ask either of those questions. People usually don't. 'Cause then they get, you know, answers.
Being truthful and honest doesn't mean volunteering massive swaths of information. It just means not lying to him, and not leading him on. If the situation changes in the future and he becomes attractive to you for whatever reason, you can deal with that then.