I've been going to the same primary care physician since 1996 (unfortunately she's retiring in a couple weeks). I have had an annual physical with her, almost always including a genital exam and a rectal exam. She has always strongly encouraged me to have the annual physicals. It's become very much a matter of routine. She allots 30 minutes of her time for the physical. Here's how it goes:
I have lab work done in advance of the appointment. On being called from the waiting room by the medical assistant, the assistant takes my height, weight, blood pressure, and checks my vision. She then updates my chart regarding my meds and family history and whether there is anything in particular to discuss with the doctor. She also does the EKG. The assistant then tells me to strip to my underpants and sit on the table to wait for the doc. Sometimes she also gives me a drape, if there is going to be a student present for the exam. That happens maybe about 25% of the time. But no drape if it's just the doc and me.
The doc then comes in. After a little small talk, we discuss whatever might be ailing me, if anything (but there's usually something to discuss even if minor). Then the doc examines my head and neck, then heart and lungs, as well as skin on my upper body. She then has me lie down, so that she can palpate my abdomen and my femoral pulses (the ones in the groin) and tibial pulse (ankle pulse). She also checks my nail beds while I'm lying down.
Next she dons her gloves, gets the tube of lube, and the card for the fecal occult blood test. I'm still lying on the table, but I know what's coming. So without prompting I take down my underwear to my knees. She examines my testicles but never my penis. She then tells me to roll over on my left side and draw my legs up. She then proceeds with the rectal exam.
While lying down, she's probably also examining the skin on my lower body, although she never makes a big deal of it. However, one time she recommended having a mole removed from my leg, which I subsequently did have done.
I then pull up my underpants and sit up. We then discuss the findings, usually emphasizing the lab work and any needed follow up. She says, “see you in six months”, and I say “thank you, bye”. And that's that. I'll miss my doc.