JoseSD,
I too have wondered and still do about that. All I can say is that in all of my time in university I have heard in passing of crafty dealings. Not something I see in business.
Let me throw out a scenario:
Universities may not have enough flexibility when it comes to getting grants or keeping top shelf researchers within their walls due to bureaucratic reasons, but could do so with a company in tow. Might look better/allow for some grants. Said grant money might have to help the economy through job/company creation. Said company may be able to help retain a high priced researcher for the university by providing stock.
A CEO of such a company maybe getting paid indirectly to do speeches or getting paid for arranging the "company's" lead researchers to do presentations, whether this may be due to using up a valuable resource(researcher) for a time and/or for the potential of accidentally letting something slip and provide competition some insight.
Some grants may have an overhead or management compensation component.
The university may itself act as a little VC.
The university may keep the lab and any new equipment HYSR had to buy during the course of the research.
Don't forget that the university branding power would increase and bragging rights for the universities involved are absolutely HUGE! That alone in the long run can pay for this research imo.
or any combination thereof.
...I can only speculate, but it seems to have worked for many others including Solar3D and its working for HYSR.