"great, you can pay them average salaries and they will be so loyal to your giant company"

The point is that they become loyal to each other, the company reaping a reward is just a side benefit of people working towards a common goal.

I was on a similar 'elite' skunkworks dev team in a company of ~ 35,000 that had executive support, and the results were insanely good. You can't manipulate people to do this; You can however give them the freedom to make it happen.