For a lack of better terms a Group […] would allow each indexed community to retain its independence

Affiliations? We’ve had those since the 90s, every fandom forum had its dedicated section for affiliates.

The people thinking solutions for these fediverse problems really need to sit back and look at the internet of the 80s and 90s. Webrings, affiliations, gopher, fanlistings, FTP, much of the problems we “seem” to have were already solved long ago.