situation with lines at Vatican Museums - tour purchased

Since you have purchased an official tour, the admission ticket is included: obviously you won't have to wait in line to buy a ticket at the counter.

Then there is the security line, so I am not sure I understand what you mean. After security, there isn't a "third line", after the usual checks you simply enter the Museums. So there can't be "a separate line for tickets/tours purchased vs. needing to buy tickets". A line for what? When you write "skip all but", what is this "all"? Nobody skips security, and there is only one security line for all visitors, unless things have changed because of Covid. I'd estimate not more than 30 minutes for that, the line moves quite quickly.

The Basilica is free, the only line is the security one. Could you easily find on gmaps the entrance of the Scavi Tour?

I’ve visited the Vatican Museums on several occasions. Each time the experience including crowds was very different. Because tickets had been purchased in advance I only needed to locate the security check line or the line for ticket holders. Although I never ever had to stand in that excessively long line that snakes along the wall and around the corner, on one occasion there was a brief wait in the ticket holders line. I did have to walk pass (or ask) folk to determine which line was the correct one but it was not an issue. On another occasion it was a ‘no lines, no wait’ situation for everyone. Procedures may have changed so feel comfortable forging ahead to obtain the information that ensures you’re positioned correctly.