These are all good points. Which is why the big picture is that the entire protocol will ultimately be curated by your grapevine. Not at first, but eventually. Every single aspect of the protocol can be replaced with something better. As many different algos for as many different contexts as you need.
The tapestry protocol, as written by me (before your grapevine takes over from me), cannot and will not be perfect. It only has to be good enough to get to the point where it can be handed off.
What constitutes “good enough”? It needs to be capable of a handful of quasi-complicated things, and transitivity is definitely one of them. I’m not an expert in all things, and I can’t hand-pick the experts in all things, but if I can pick the people who pick the people who pick the people etc who are experts in some particular thing, then i can delegate anything and everything to a small handful of people who will probably be pretty good choices for the topic in question. And if it’s not controversial, my grapevine and your grapevine will probably settle on the same small handful of people who know and care about the topic in question. Or at least their opinions will likely overlap. I’m thinking about niche questions about our digital tools of communication, like whether a nostr note timestamp should use created_at or createdAt. No one really cares, provided we’re all on the same page, and the grapevine will usually get us all on the same page. (Unless there is controversy, which there isn’t in most cases.)
Other than transitivity, management of category trees by my grapevine is another one of the quasi-complicated but necessary things, I think. Which is why that’s also in the tapestry protocol, and goes by the acronym DCoG: decentralized curation of graphs.