In 1.1 with the new related sites, is it intentional that MSO and SO are not related?
Meta.StackOverflow is a meta in name only. It is not Stack Overflow's meta, at least not from the API's perspective.
Its a tad confusing, I know. Its a consequence of the "per-site meta" concept being introduced long after meta.SO existed.
I would assume the answer is Yes.
Although Meta Stack Overflow is a Meta site, it is also the "capital" for the Stack Exchange engine as a whole, and unlike all the other Meta's also has individual reputation per user. It is really a special Meta site.