What's in it for MS?
They get all of those young hearts and minds. Remember that the Pi was originally developed to get school children interested in computing and thus developed contacts in the schools. So MS gets to take advantage of those contacts.
Back in the day, Apple was giving their early versions to schools free of charge to get the youngsters familiar with their system before they ever got into the working world where corporate computing was happening. This is, essentially, the same marketing technique on the Pi.
"The pitch from Microsoft is they’ve got great tooling to get it started..." Sure and a great marketing opportunity with the marketing channel already opened up by the Pi developers. And the opportunity to get the kids started on using their development tools.