It's all about making sure the patient is comfortable, really, combined with the fact that the expected way of going about things is to complain about an issue and get referred to a specialist who can actually do something about it.
Answer the questionnaire, hand it to the nurse, get vitals taken (shoes off for height and weight), talk to doc about how meds are working, stethoscope over clothes (sometimes up the back of the shirt), lie down and get stomach felt with the doc reaching under the shirt.
Reflexes can be done over pants but I haven't had that done since, like, childhood. Obviously you don't need to get undressed to have a doctor look in your ears and mouth, either.
There's a whole thing about not wanting patients to be uncomfortable or feel vulnerable, that's how you get people dying because they don't like the doctor and don't get help (combined with that whole “health insurance” bs, of course).
And it's starting to be suspected that thorough yearly physicals are just a waste of time. There was also an article that talked about running too many tests found too many things they couldn't just leave alone, sending a patient through months (or years with how far out I have to schedule some appointments) of appointments and thousands of dollars to treat an “issue” that wasn't causing problems that they didn't come in for.
I did get all the way undressed (socks on even if the floors seem clean) for an x-ray the other month though and had to take my pants off (socks and underwear on) for a knee x-ray. Haven't had an obgyn appointment in many years though (no reason to, not sexually active, no personal concerns with my health) but I think I had to strip and put a gown on for that, too.
There's plenty of reasons to be told to completely strip, but you're unlikely to be without a gown (local system got fancy new cloth gowns a couple years back to replace the weird itchy fabric ones), and it's very unlikely you'll be undressed for a yearly checkup unless your doc notices your chart & says you're a few years overdue for a pap smear and might as well do it while you're there.
Okay rambling for the night done.