For instance, I would say that rationalists are much "closer in memespace" to transhumanists and effective altruists than they are to "alternative approaches to wellness," but that doesn't seem to be what this shows.

I don't think the map is trying to use space that way. E.g. LGBTQ culture isn't all that close to Computer Scientists in memespace either; they just happen to be next to each other on the map because of the way the various arrows and stuff worked out.