> ... even though the user wants them separate ...
Which "the user" is this? The same user that uses GitHub's OAuth as single-sign-on credentials for other partnering sites like TravisCI, etc? If I was in the MS ecosystem and already had an identity that I could re-use (and didn't already have a GH account), I'd probably use that, just like those who login to various websites with their Google, Facebook, Amazon, or even Twitter SSO identities. I don't see how expanding SSO to Microsoft accounts would hurt anyone.
You may not see why people would want separate accounts, but many people do. Sometimes the accounts are for different legal entities, such as work, personal, and for helping a charity. It is not correct to arbitrarily merge those.
Also, there may be different pay structures and packages used to pay for the services for each of those accounts. Hopefully, you can see how merging these can create far more work for the user, even when there are many cases that have negative benefit.
Which "the user" is this? The same user that uses GitHub's OAuth as single-sign-on credentials for other partnering sites like TravisCI, etc? If I was in the MS ecosystem and already had an identity that I could re-use (and didn't already have a GH account), I'd probably use that, just like those who login to various websites with their Google, Facebook, Amazon, or even Twitter SSO identities. I don't see how expanding SSO to Microsoft accounts would hurt anyone.