I know that a number of others have already responded, but to add in another experience based reply for OP, yes this is completely normal. My wife and I have custody of our nephew; I take him to his yearly physical. His pediatrician has done a genital exam on him each year. For the first couple of years it was a pretty quick check, long enough to make sure he didn’t have a hernia and that his testicles were descended. His underwear would be down 10-15 seconds max.
This past summer that part of his physical was a bit longer. She checked his penis and foreskin, checked both of his testes for lumps, as well as the hernia check, and talked with him a little bit about puberty. This is also what I remember experiencing as a kid/teen seeing the pediatrician growing up.
I think the thing your son’s pediatrician could have done better was communicate with you and your son. My nephew’s pediatrician sent us a note through MyChart when we scheduled his appointment letting my wife and I know that this year his exam would be a bit more thorough, and she recommended that we talk to him beforehand so he wouldn’t be caught off guard. But even a heads up before the exam started on the day of would have been better than the 5 seconds of warning you got when she asked your daughter to step out.