We received confirmation of our Scavi Excavations tour by email (yeah). It is at 3:45 in the afternoon in late July. I don't know if we should reserve the Vatican museum at 9 am and count on being able to take the short cut into St peters from the Sistene chapel or get to St Peters early before the crowds and book the museum later but before the 3:45 tour.
Unless you book a tour of the museums you cannot count on being able to use the tour door. Sometimes people get through but for the most part there is a guard there checking tickets to make sure you are allowed to use this bypass. If your scavi tour is at 3:45 pm a tour or entry tickets to the museums at 9am will give you plenty of time to see the museums and get to the entry to the scavi tour. I wouldn't worry about it too much. It will also give you time to visit the basilica if you choose, check any bags you have that won't be allowed on the tour and get some lunch. Donna