You are right that orthos would not check for STDs with septic joint-- it is too late. You missed your chance to catch/cure it earlier. (malpractice?)
Gonorrhea STD that is untreated is the number one cause of a single hot joint. There are almost 1 million new cases per year of Gonorrhea and most common 16-24yo. Most STDs don't cause hot joint but most single hot joints come from STDs- gonorrhea. Delay of diagnosis --waiting for joint to become septic is 10% fatal and a malpractice attorneys dream. Once septic it is almost too late to prevent joint damage. STD (urethral) gonorrhea could have been cured with a pill and a single shot of antibiotics, Now due to untreated STD the patient needs surgical drainage irrigation and IV antibiotics--- which are becoming less effective (some drug resistant std now exist.) and possible loss of joint.
I don't know what happened and I don't know that doctor nor do I have an opinion about Jim Jordan but I do know that college kids get STDs (high prevalence) and wrestlers often have swollen joints. Screening is valuable with a high prevalence of the focused disease. I am not saying every kid needs a GU exam/work up for every visit and this doctor sounds strange but you don't know what happened and neither do I but checking a sexually active college kids penis for a swollen joint is within the realm of evidence based medicine.
Your position sounds like you advocate skipping that whole physical exam/disease prevention/early intervention thing of modern medicine. You can just wait and see right?? Let the chips fall where they may. No surveillance. No early intervention. Vaccines are for wimps!! Your wife should not get annual breast exams, mammograms or pap smears cuz that is uncomfortable/embarrassing. Wait for the Lump to appear (one in 9 women get breast cancer). No colonoscopy cuz that is just gross. Wait til you crap blood with liver metastasis. No digital rectal prostate screening cuz that is weird. wait til your back hurts from bone metastasis. Be a man/woman and play the card you are dealt. Sorry, not for my family.
I will say that if some of the allegation are true the doctor was strange and should have had his license pulled/suspended. i.e. Doctors don't shower with their patients.
BTW I bet your "professional training" was not medical school.