Every doctor is different on this. Any doctor who has ever seen a trans patient before or is aware of it may know that there are things like binders and packers, and any doctor who has NEVER seen a trans patient, is aware that patients may have atypical body parts, marks, scars, or other 'under garments' that they are self-conscious about.
My endo did give me a fairly comprehensive physical before precribing T. He had me change out of my clothing and put on a doctor's office gown, but I left on my underwear and packer. One thing I liked was that he minimized the amount of time I was undressed. He spoke to me first, had me change in private, then examined me for the stuff he wanted me more undressed for, and then had me get dressed again before we talked and he wrote scripts and whatnot. When all that's happening is blood work, blood pressure being taken or even injections given, the only thing I remove is what is absolutely necessary (pulling down pants a little, rolling up sleeve, etc.).
An trans-experienced dr. is more likely to get that minimizing the amount/time of undress is important. If your dr. doesn't know this, though, you prob should mention it and ask to have as little undress as necessary and whatever modesty "gown" they have, and not to spend the whole time like that.
