My experience is that in a complete physical includes for a hernia and prostate and the doctor is more concerned about not being present when I undress than when I am naked and getting examined. Prior to the exam the nurse asks me to strip down to my shorts. Maybe Ill just start out naked rather than in my shorts next time so the doctor doesn't need to leave the room.
Now that I go to urologist and dermatologist annually, my primary doctor doesn't have me undress at all. He even listens to my lungs and heart with my shirt on!
Urologist has me stay dressed until he arrives and then tells me to drop my pants and underwear for the exam. I don't wear underwear and he has never mentioned the lack of it.
Dermatologist's assistant tells me to strip to my underwear so I wear it when I go there, even though I never do otherwise. When the doctor comes in, after he has checked the rest of my body, he looks inside my underwear but does not have me remove it.
For the cardiologist, I say I am more comfortable shirtless for he EKG than with a rolled up shirt, so I take my shirt off and leave it off for the rest of the exam.
I have a great doctor who was more concerned about how I felt the first time he had to do a complete annual skin survey. He asked me to take my t-shirt off, then put it back on then take my shorts off, examined me and then asked me to lower my underwear. A year later, for my second annual skin survey, the same routine started, and instead of putting my shirt back on I asked him if it wouldn't be easier for both of us if I just got naked. He laughed and said yes, so I stripped, he did the exam and then I sat down on the exam table and remained naked while we chatted about my health in general and he entered notes on his computer. We chatted briefly about our respective summer holiday plans then I started putting my clothes back on. Since then, when I go in for my skin scan, I just start undressing when he comes in the exam room.
I see my Dr about once a month for blood preasure checks. She always starts to listen to my heart and lungs through my shirt but always ask if she can lift it up to hear better. I would just take it off but not sure of her comfortablity. For my physical, the first year she told me that they usually have patients put gowns on but the one size fits all doesnt apply to me so I kept my cloths on for the bulk of the exam. Last year and this, when it came time for the below the waist, she said to just drop my pants to my ankles. She turned her back to prep the table and I just took my pants off and assumed the position. I think because I was so comfortable being exposed, she did examine my testicals, penis and hernia. She had also said that there was supposed to be another person in there with us but I dont think the assistants wanted any part of my exam.
Its easy for me. My Dr is a friend of mine and a Urologist. I show up and go down to just a jockstrap. He and his staff, all guys, have seen me in it and it makes life easy. He has access to check my equipment up front and also out back for the prostate exam, which he does twice a year since I had a nasty infection in mine.