My pediatrician would always do an exam with me in my underwear. When I was very young (5 or 6, probably even younger.) he would pull out the waistband and have a quick look and make sure both my testicles were where they were supposed to be. As I got older, he would pull my briefs down, check for hernias and foreskin retractability (and, I assume, hygiene.) Once puberty hit, the genital exams became slightly more involved, mainly feeling my balls for abnormalities, size, growth rate, etc. Pretty much evolving into an adult exam, (Minus the rectal exam.)
The reason for the "double standard" is very simple.Boys genitals are external, girls are internal. Add to that the fact that, at least when I was a kid, playing could get pretty rough and tumble, not to mention that boy's bikes have crossbars, and girls bikes don't. I remember a few times stopping short and ending up on the crossbar. (Thankfully, no damage done.).