Each of your points of concern addressed:
- I'm not as short as you, but I have met guys as short as you who have no trouble being seen as guys. With height, it is more of a confidence thing. Will some people think it's weird that you're so short? Sure. Will it ultimately matter? No. Just own your shortness. Make a joke out of it and laugh it off.
- You are probably genetically predisposed to balding. You could ask your doctor for Finasteride to try to offset the T, but I'm not an expert on it so it may or may not be effective in your case. But a lot of men in general experience male pattern baldness. So balding is a fairly "male" experience that you could have in that sense.
- Bottom surgery is pretty good these days. The only time I ever hear negative opinions expressed is from guys who haven't had it. Do more research on it before you come to any conclusions about it. There is a stupid amount of misinformation out there from people who frankly have no business speaking on it.
- Most guys end up having top surgery, so not sure why a large chest would be an issue to transitioning. I had a large chest before I transitioned too, now I'm flat.
Now. I'm not intersex that I know of, and I have no inclination to find out if I am. But if you feel uncomfortable with your body to the point that you are considering transitioning, do you necessarily need to speak to a geneticist to confirm your intersex status? Hormone levels drive HRT dosage, so not really likely that your genes will matter for that. I also don't think I've ever read that intersex people can't have any kind of surgery, so top surgery and SRS wouldn't be ruled out for you on that basis.
Aside from potentially being intersex, it sounds like you're doing the same kinds of questioning that everyone does before they decide whether or not to transition. I can't tell you whether or not transition is right for you. I also won't tell you to give HRT a shot if you're not 100% sure about it, because T is the stronger hormone and has many irreversible changes. I will say that almost everyone is unsure at the stage you're at, so you're not alone in that regard.
I would spend some time doing more research. Perhaps also talking to a therapist about your concerns. And then weigh the pros and cons. If you're uncomfortable now and don't care about alienating your family, you don't have too much to lose by giving it a shot, but there may be other circumstances in your life that you need to account for before you make a decision.