Your endo will do things their way. Not all endos do the same things in the same order.
Blood will be taken. Look away, that is what I do. Ask to know when it is done and the blood is gone. A little blood is a price almost all of us must pay.
As for a physical, perhaps... although endos are more concerned with blood, a GP may be more likely to give a physical. Blood tests can really provide a great amount of info about your current health.
Congrats, and good luck.