Just to be clear, when the tour operator quotes a price that does not include cost of entrance to the site, does this mean that we have to make our reservations/buy our ticket ourselves for entrance and then meet up with the tour operator?
Good question. I'd recommend asking that of the individual tour operators just to be safe.
Generally not but I'd ask the question just to be sure. I did a tour of the Vatican and we met up looked around St Peters Square and then went to line up for the Museums. Once inside we lined up and each bought our own ticket and then regrouped and continued the tour.