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The patient, not the doctor, ultimately decides which parts of the examination are performed. Without the patient communicating symptoms, doctors may not identify any illnesses during a physical exam. The only scientifically valid components of a physical exam are laboratory tests like blood work and urinalysis. Instead of reporting any pains or illnesses during your next physical, see if the doctor can identify anything through their examination.
Additionally, many invasive examinations are not endorsed by medical associations such as the AMA or ACP. This has been widely documented for over 15 years.