Ok let's try approaching this a different way for a moment. If all of that $1.8M in your example went to the electron microscope, and there was no overhead, how would any of the following be funded:
- the building housing the scope?
- The electricity used by the scope (non-negligible in this case)
- The staff to run it
- training to use it
- maintenece
- hr/legal/accounting services regarding the grant itself?
Furhter, without the above services, not only do you need to fund that stuff, you must now take time away from actually researching to hire those people (for free!), to manage those people and resources, and essentially not do science in order to save science from the evil humanities leeches.
My point, and the point you are conveniently being a disingenuous about, is that you can't just take some money and "do science" there is always going to be other factors necessarily involved.
As for proof of universities vs companies: I can only offer anecdotal evidence, but it is pretty strong. We do lots of research for various government groups, and I find it telling that when we first started working with the DOE on big grants, the were shocked at our overhead rates, which are half the national labs, and much less than other companies. Yet they are happy with our level of research, and have given us more research because they get a better "bang for their buck".
Similarly we had some pretty specialized work that needed to be done for one of our projects, so we considered having SAIC or Honeywell do some of that work. We couldn't because to get one engineer for 50% (half of every work day for a year) cost $500K (after overhead). For that we instead hire a good engineer, an appropriate work environment for him, and still had $200K to more tasks down the road. (not to mention the ability to get more grants in which that work is done now).