It would be nice if you could go back and link materials in model sets afterward. Another option related would be to let the user do something like Link and Apply materials from [X] model set.
It would also be nice to have some sort of visual cue that a model set has linked materials. It's always a sad day applying materials to another model set, only to realize they were linked later. (this happens occasionally when we hand off work between coworkers)
Solo mode and linking via scene materials might help to get this quick done.