Having conducted medicals in the army, I always retracted the foreskin in uncircumcised men, it's part of a thorough examination, you need to check for retractibility, infections and abnormalities such as hypospadias/epispadias. In the military, venereal disease is an issue, so you'd be particularly vigilant for signs of gonorrhea, herpes or syphilis so you need to look at the urinary meatus and under the foreskin. To fail to check under the foreskin in a complete medical is negligent in my view, in the same way as it would be negligent not to examine lymph nodes.
Art - good point that you raised on narration. I always told patients what I was going to do in every part of an exam, it's a form of courtesy and is more empowering because you're informing them of what you're doing to their bodies. Nothing irks me more than doctors, medics and other health professionals who just grunt out orders of 'stick out your tongue', 'lift up your arms' etc and nothing more. I remember one guy going 'aawwww, that's what it's for' when I explained why I was cupping his testes and asking him to cough, he'd had this done in numerous other army medicals and had no idea why they grabbing his nuts other than they were sadists. Checking for hernias was the last thing he'd have thought of.