My brother and I went to the same pediatrician growing up and our physicals were pretty similar. The only difference was that my brother (who played sports in high school) got checked for a hernia and I did not.
We both had to strip down to our underwear from the beginning. At the end, we would be lying down on the exam table and he would completely remove our underwear and have us be naked for the genital exam. While we were lying down naked, he would look through our public hair and thoroughly examine and palpate our penis, testicles, and scrotum. After this, the exam would end for me and I was allowed to get dressed but my brother had to stand naked and cough twice for the hernia check.
On the other hand, a friend of mine from college had his sports physicals at his high school's nurse's office. He only had to slide his underwear down briefly turn his head and cough for a hernia check; he didn't have an extensive genital exam.
How common is it to have a genital exam without being checked for a hernia? How often is it done the other way around?