There are at least two lines outside the Vatican Museums. One is for people hoping to buy tickets; the other is for folks with online reservations (which need to be converted into physical tickets inside). There is a line minder who sends in groups of people with entry reservations more or less based on the time of those reservations, but not all in one large group because they don't want to overwhelm the ticket lobby. From time to time some people from the buying-tickets line are sent in.
There may or may not be some other arrangement for people on tours. (I suspect the guide can convert the entire batch of reservations into tickets so the clients don't all have to line up, but I don't know for sure.)
I had no significant issue with the line for people who had reserved entry times in advance; I wasn't in that line for long. I just don't see why the Museums have a system that (at least as of early 2023) requires people with reservations to pick one of several ticket windows in the lobby and stand in line to get a ticket that will open the turnstile. If you happen to pick a line behind some people who are buying tickets rather than swapping vouchers for tickets and they are confused or having trouble with their credit cards, it would be irritating. It's always more efficient to have a single line feeding multiple windows, but there may be insufficient space in the VM lobby to pull that off.