Hrm, even the top universities that make their own masks are only doing it for truly, truly ancient process techs like 350nm -- and it's done by the people researching lithography and MEMS, not the people researching chip design. I haven't heard of any university fabbing a mask themselves that was for an actual microprocessor in the last decade.
The research groups that do chip and circuit design sometimes have deals with the commercial fabs and maskmakers. But these are really icky agreements if you look at them up close (which you can't since they're kept secret). It's usually an unspoken "you send us smart grad students as summer interns and we'll make masks for you at a loss" sort of deal. The companies are certainly losing money on it; they do it because they're getting some sort of other benefit.