He is the perfect transition guy, who is likely going to be replaced in a few years time when MS decide they want to capitalize on the money they spend on a un-profitable but popular service.

Which is a pattern we have seen from their takeover of hotmail and more recently with skype, where they also waited a few years before starting the transition from independent brand to a sub brand under one of Microsoft estates.

What you are going to see when MS is done integrating the leadership of github into MSFT and Nat have been replaced by a next phase CEO, is that githubs CI hooks will become more and more symbiotic with azure, and the a lot of the documentation tools offered will hook directly into office365 tools, which will require a synchronization of accounts with MS other SaaS offerings.