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.

I'm not entirely sure that thinking of yourself in terms of position relative to various subcultures is altogether a good thing-- Keep Your Identity Small and all that.

Memes seem worth studying in general if you have memes you want to spread. Not thinking about memes and subcultures because they're tangentially related to identity, which can compromise one's rationality, seems like not studying economics because it's tangentially related to politics, which can also compromise one's rationality. But this could be a good caution. It's worth noting that not everyone agrees with PG on identity (another).

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. Is there a more sophisticated explanation for the positions of the various groups on here and the sizes of the boxes and text that I'm missing?

There's a lot of overlap between transhumanists and effective altruists, but that doesn't mean that the relevant memes share the same history?