I have some news. Things have changed at the Vatican Museums. I'm sorry I can't provide a more precise and complete report, but I was still severely sleep-deprived and jetlagged when I went to the Museums yesterday (Day 3 of my trip).
I observed at least two points at which there was a separate area for Get Your Guide clients. I think the first was in the large hall where you swap your voucher for an entry ticket. I guess that means the GYG folks didn't have to queue at the regular windows. If the GYG counter was adequately staffed (I didn't notice), that would save quite a few minutes. The best I could tell, the regular windows served folks from the don't-have-a-ticket line as well as those of us who had paid for entry but needed to convert the voucher into a ticket. There were some people from that other line let into the building just as I got in, and we all seemed to be headed in the same direction; the difference is that I had essentially no wait to get into the building, whereas the no-ticket line was long and moving very slowly.
When I walked in there was a line of perhaps 8 to 12 people at each regular ticket window. There was no way of knowing how many of the people in each line were conducting the more complex transaction of buying a ticket or otherwise were going to need more time. So choosing a fast-moving line was pretty much blind luck. I definitely got hung up in the ticket pick-up line for at least ten minutes.
Philosophical question: Can we say buying a ticket (which turns out to be just a voucher) online in advance means you skip the ticket line when you still have to line up to convert said voucher into a ticket? You don't get to skip the line; you just reach the back of that line a lot faster.
After picking up a physical ticket you go upstairs toward the museum entry point, first passing the area where audioguides are distributed. There was a separate Get Your Guide counter there as well. It only took a couple of minutes for me to pick up my pre-purchased audioguide at the regular counter, so I don't think being a Get Your Guide customer would make much difference there.
I vaguely wondered at the time why the Vatican had made a special deal with Get Your Guide. All credit to the GYG person who negotiated that arrangement.
No one cared about my full water bottle, and no one cared that I was very early--originally by 50 minutes or so. I was still probably 25 minutes early at the point of picking up my audio guide. I don't know whether there's a limit to how early they'll let you in; the person converting vouchers into tickets can definitely see the reserved time slot on the voucher.
I don't really recommend the audio guide except for someone with vision so compromised that reading the posted descriptions is impossible. When I sought info on exhibits flagged as being covered by the audioguide, I got brief explanations that appeared to be taken from the material posted nearby. To make matters worse, my guide stopped working about halfway through. The Museums are so large, it's totally impractical to return to the pick-up point for a replacement.
I didn't take any of fhe posted shortcuts. My total time inside the Museums was between 4-1/2 and 5 hours. I was very selective in what I really looked at, and two of the exhibitions I was especially interested in were at least partially closed off. And I have very little interest in classical sculpture. Sculpture lovers would benefit from having the entire day.
I got the impression they had fiddled with the route through the Museums, though I could be mistaken about that. I'd recommend not assuming Rick's description of the route matches current reality. The final turn up (or maybe down?) the stairs to the Pinacoteca wasn't well marked. Stay on your toes if you want to see it.
You can see other parts of the Museums after the Chapel, but good luck finding your way, and some areas may be inaccessible.
.