Meta Stack Exchange is not a per-site meta. Think of it as a Stack Exchange main site about Stack Exchange itself -- encompassing Stack exchange operations and hundreds of SE-operated sites.
See "The future of meta.stackoverflow and meta.stackexchange", and its linked and related posts, for more information.
If you have questions and/or expertise about almost anything Stack Exchange (that's beyond a per-site meta's scope), then Meta Stack Exchange is where you go.
It's like apple.stackexchange.com, only for Stack Exchange.
Yes, Meta Stack Exchange is not a perfect "Main" site -- in that it has a bit of a meta culture (a lower fact/opinion ratio, for one) but it's more main site than meta and is treated as such on all the utility pages, and in SEDE and the API.
Meta Stack Exchange is also not the only "main" site to be its own per-site meta. Stack Apps is another example of that (and Area 51 has no per-site meta).
See also, the per-site-meta tag on Meta Stack Exchange.