If you allow the NCAA to schedule your travel then you are subject to their rules. Smaller schools like CSU will use the NCAA for travel because it saves them money. Many (but not all) larger schools just eat the travel costs and set their own schedule and itenary. However the hotel is almost always set up by the NCAA unless their is an issue.
I can’t speak for the rest of the country or what other schools did but the one I was involved with , and yes it was a major university, used the ncaa travel itineraries and it worked great. We never had an issue. The ncaa flights were great as they were paid for by the ncaa and they use larger airplanes so the entire travel party could go on the same plane- players, coaches, team staff, AD administration, cheer, band- everyone.
The ncaa hotel situation is pretty straight forward- in each city that there are games in the ncaa contracts with hotels that are full service only- full service hotels is essential because they have ample meeting room space and full service kitchens for catering meals in house. Typically each team gets their own hotel, unless there isn’t enough full service hotels then teams share the hotels. The ncaa also has a hotel for their personnel and referees and do not stay at same hotels as teams. Also something of note is that the hotels are ranked and the highest seeded team gets the best hotel and the subsequent teams get the lesser of the hotels.