I was involved in the project of building a new website for my university. The previous site ran in joomla while new one was to run in drupal. The sitemap was partly created from ground up, like the main page, but a lot of content was to be transferred from the old site. Some of this old content was modified while a lot of new content was added. I guess I could say that the front end was mostly handled by a creative agency while the back end was handled by the IT and the content was mostly handled by individual administrations.
In my opinion the process of content creation in an institution such ym university worked a bit ineffective in my opinion. The decisions of what content the site should host, how the sections and menus would be like was formed mainly by people who had no idea what a UX is and how a website should navigate. Of course there was professional opinion on the top level such as the main page, but much of the subdomains, like individual collages or schools, decided on what to have on their micro sites themselves. It would be pretty hard to get all of these sections' desires in a centralized system or have the professionals decide what to have on the website. So they had every Office of Dean decide what they wanted. This turned out to be "good" for some, "bad" for others.
But I think the main problem in a process like this was that there wasn't a single party doing all the work. As far as I've observed it was always back and forth as with most big projects. Though, there are successful examples such as the MIT website where my guess is everything is being handled by the IT, since the people in the administration would be aware of the fact that they know how things should be.
About the fees, I guess it could be both of those reasons depending on the motives of the university.