The MS - for - startups page is pretty clear that Microsoft wants the startups they help to be helpful for _their_ customers down the road. So they want the startup to ideally play nicely with Azure / Office365 / GitHub / other Microsoft properties.

The funding thing is a bit restrictive (speaking as a currently-bootstrapping founder), but I understand that it would be very challenging filtering out scammers and not-serious users otherwise. It's easy to put up a nice-looking website and then spend the (pretty generous) credits on unrelated work.

I don't think anything here is especially nefarious, given how public they are about the restrictions and goals. Think of it as closer to an accelerator than a charity, if it helps frame the program better in your mind.