I don't have the exact timeline at hand, but Microsoft Accounts (originally Microsoft Passport) as a Microsoft service wide SSO were originally cooked up at Microsoft, while Hotmail was a separate service that Microsoft acquired. And this was in the late 1990s. I guess they originally designed the account system to be independent of the whole web portal nonsense that was fashionable at the time.

...anyway, I think it's good thing that Microsoft let you use whatever email address you want with it and not force you to use Hotmail/Outlook.