OK, interesting. We'll have to play around with this.
The reason I was considering model courses is I set up WeBWorK courses every semester for the same collection of 5 or 6 courses. In the past I've copied templates from the previous iteration of that course, but this generates a lot of clutter over time.
It seemed to me that from an administration point of view it might be simpler to have a model course for each of the courses that runs regularly on our server, and then every time I create that course for a new semester, I could use the model for that course. This would mean that in addition to problem sets, things like the welcome message would be set in advance. (This is something I end up doing for most people when I create their course.)