Questions about why Stack Overflow does not share rep with Meta Stack Overflow are met with the response that meta.stackoverflow and stackoverflow do not share a "parent-child relationship" like the other meta sites. For example, this response:
Stack Overflow isn't in a parent-child relationship with Meta Stack Overflow like the other sites are with their respective sites. Meta Stack Overflow is intended to handle not only issues with Stack Overflow, but for the Stack Exchange Network as a whole. It is also the specific place to ask questions about Data Explorer, Area 51, and Careers which otherwise lack their own meta sites and even reputation in some cases. In essence - Meta Stack Overflow is the site for all of the Stack Exchange Network. Tying reputation to Stack Overflow would undermine that, since not everyone who knows the engine is particularly active on Stack Overflow.
This just raises the question: Why doesn't Stack Overflow have a "real" meta (with a "parent-child" relationship) like the other Stack Exchange sites? Why is it treated as a special case? The closest thing I've seen to an explanation is this bit from the New Per-Site Metas blog post:
For now we are leaving meta.stackoverflow.com grandfathered in, as-is, with no changes; it’s still a standalone community with a standalone reputation system. We think Stack Overflow is large enough to justify this, and it just so happens that Stack Overflow is also the name of the company, too. Meta Stack Overflow will serve as the “National Capital” where we process feedback not just for Stack Overflow but for the core engine itself — while the smaller meta sites are akin to regional or state capitals.
But this is a really unsatisfying explanation as it doesn't really stand up to reason. How does the fact that Stack Overflow is large justify the lack of a "real" meta site? If anything, shouldn't the fact that it's large actually mean the opposite: that its meta should not have some purpose?
Despite all of the negativity towards this suggestion, it looks like it actually got implemented: Announcing The Launch Of Meta Stack Exchange