I've experienced a wide variety of the way I've been dressed during a physical. Fully clothed, undressed to underwear, gown, etc. My current PCP leaves me fully clothed. He raises my shirt a little to listen to my lungs and heart, and raises it completely while he performs the abdominal exam with me on my back. He then instructs me to stand and drop my pants for the genital and rectal exams.
In RL, I think I prefer this method. It keeps me warmer in the always freezing exam room. It's easier for me since I don't have to take the time and effort to undress then redress. It's slightly less embarrassing since I'm not exposed the entire time and self conscious of all my skin and fat and moles and all my other imperfections. The power dynamics aren't shifted nearly as much between myself and the doctor since we are both dressed during the interview and exam. All this and it's still easy, quick, and efficient to expose what needs to be seen or accessed.
From my medfet perspective, the benefits of staying dressed are that I still don't know if I will have to expose myself to the doctor or not. I love the nervous anticipation of the unknown during a physical. For example, my current doctor performed a genital and prostate exam during my first 2 yearly physicals with him, but didn't do either during my third physical. So in a couple of months when I go back for my fourth annual exam, I don't know if I'll have to intimately expose myself to him or not until the time comes in the exam. I like this feeling. A mixture of dread, anticipation, nervousness, excitement, arousal, and embarrassment. The other nice thing about remaining dressed is I enjoy actually unfastening and lowering my pants in front of the doctor. It's extremely embarrassing during the exam and I get no pleasure from it at the time. However, embarrassment is a big part of my medfet, and after the exam it is mostly what I focus on in my fantasies.
However, also from a medfet perspective, I'm not sure I actually have a preference. I see pros and cons of the all the different levels and options of dress\ undress during an exam. My medfet fantasies evolve from actual events and experiences during medical settings. So it all contributes to my memories and fantasies. What I'm wearing is just one part of the equation. How I'm told to undress, who tells me, and at what time are also important. And these are all things that I can alter and experiment with in my mind while I'm fantasizing.