I am reminded of my experience in high school.
When I was a kid, the usual attire for us during summer was levis and a T shirt. My mother had told me that she wanted me to wear something more substantial than a T shirt so that people could not see how thin I was. Also, at that time, I was smaller than most kids my age.
In gym class, teams were designated by having one team remove their shirts. You can imagine how I felt since I was smaller and was also embarrased because my mother made me believe that I was unacceptably skinny. So, a guy need not be totally nude to feel uncomfortable undraped. Interestingly, when I was a preppy, guys used to say, "For such a little guy, he sure has a big cock." So, I certainly was not deficient in that area, but was in other areas.
At the earliest opportunity, I took up weight lifting, which totally solved my body image problem. But there are parts of the body that cannot be developed through exercise, so I guess that I can see why some guys might feel uncomfortable nude. For me, being totally nude in gym class was not much worse than being shirtless, except for the fear of getting an erection, which actually happened once.