MS owning GitHub is a very recent thing in GitHub's development, so that isn't really a good comparison. I doubt getting bought by MS was anything like the plan in the early days!

> Spolsky is former MS and familiar with their stack

That is key: often experience (i.e. the cost of problems caused by lack of experience) can outweigh licensing considerations, particularly in the fast moving PoC/prototype stages and the subsequent quick growth phase.

> Additionally, SQL Server is a very good database

No argument there. While other DBs could certainly do the job too, SQL server is a good choice, even without that "experience bonus".