We are with a group getting one of those after-hours entries to the Sistine Chapel and Vatican museums. My sense is the museums may limit the total time, bur can't tell if that limit is coming from the museums or from our group. Also, not sure how much freedom there is to look around in the museums during that time. For instance, if your group isn't slated to see the Raphael rooms, can you break off and see them, or does the museum require groups to stay together?
If you are going with an after hours tour group you'll need to stay with the tour the entire time. You will not be able to go on your own and your group will be restricted to a certain route they must take. If you leave your group there can be serious repercussions as not all of the rooms are open and they don't want individuals walking around unsupervised among the artwork. If you are talking about the Friday nights at the Museums then there are only certain rooms that are open but you'll be able to visit them if you wish. If you are on a tour for Friday nights you'll want to stay on the tour unless there is an open room not covered by it. If that's the case then you might not want to take the tour. Donna