Update.
Recently had my 40 year physical. No one believes I'm 40, but that's another story...
Nurse told me to strip completely and put on the gown, that the doc will examine my whole body.
Doc comes in and says she is going to check me out from head to toe. First she checked eyes, ears, mouth, neck. Checked heart rate, breathing and lungs, then had me lay down and pressed my abs. She then told me to stand next to her, facing the same direction she was. She lifted the gown and said she was going to feel my testicles for unusual lumps, but first she slightly retracted my foreskin and squished the glans at the opening, then put the skin back and let go. She was quick to move on to the testicles for what was probably the gentlest exam they've ever had. Then she followed with the least intrusive hernia check I've had (a common theme among my female docs). Male docs have always stuck a finger up through my sack and into my groin, quite uncomfortable. Female docs seem content to just hold their hands on my pubic area while asking me to cough, or like my current doc, she just held my testicles in one hand while touching along the upper scrotum with the other.
Then she did a skin check from head to toe, spending the most time on face, neck, shoulders and arms, quickly going over everything else under the gown again.
I like my doctor, she's very professional, but I sometimes get the impression she is a bit uncomfortable with male patients (or at least with me for some reason). She did discuss sexual activity and whether I use protection, prostate health checks (which she did not physically examine, perhaps because I had the biopsy in Sept.), other injuries and past ailments from my record, but I didn't really feel like this was a full on 40 year physical or even a very thorough standard annual exam.