I'm not sure that the technology running in the backend is really relevant here. If anything having "objective" third parties using your technology seems like a better selling argument for .Net than having it in-house.

They would lose a paying customer ;)

Looking at Microsoft's strategy I doubt they would care whether it runs on .Net or something else. They would look into integrating with Azure (lots of Linux) and GitHub (R-o-R) as well as SO Jobs with LinkedIn (Java(?))

Well, that customer is paying those licenses from their own income. By acquiring $customer you can get all of their revenue and not just the part they currently spend on licenses.

True and I wasn't fully serious. But: Having SO as an external showcase has benefits for attracting other customers over "we use it on our site" A testimony from an internal customer is less valuable as I see more company politics over technical reasoning.

It depends how you measure. But my company runs .NET at a much bigger scale (in terms of http requests and infrastructure footprint) than SO and I doubt that we are the only ones.