A certain amount of duplication between sites is fine -- in my estimation about 10 to 15 percent.
I know some members of our community go absolutely bonkers if they see any duplication of any content of any kind, but... I don't agree with these folks. :)
So, it is OK as long as it's not overwhelming the topic-specific ("child") metas, and right now it's a tiny fraction of the questions on those topic-specific metas. So not worth worrying about at the moment.
Also, bear in mind that not all sites will survive beta, so they don't get network privileges -- including question migration rights -- until they've proven they can survive.
In general metas are black (grey?) holes -- once something gets migrated to meta, that's it, it can't be migrated anywhere else. This is 100% intentional, and all metas will behave this way.
(yes, you could make a case that we should support migrate-to-meta-so since that's the "national capital", perhaps.. but it feels risky to me.)