The main map uses 2 of the 13 underlying dimensions, and is especially constrained horizontally, so yeah, some of the specific pairwise juxtapositions aren't totally indicative of overall similarity.  

You can get a slightly better sense of the local neighborhood around any specific genre by looking at the little inset map at the bottom of the genre's own page, e.g.:  

everynoise.com/engenremap-metropopolis.html#tunnel

(accidentally left this out…)  

This cohesive playlist runs right down the middle of these three genres IMO:
open.spotify.com/user/assiagrazioli/playlist/7Gl2RCegZJ5Im1bZY9iHHY

Hi Glenn, big a fan of yours since the early echonest posts.  

One thing that strikes me, picking up on "metropolis" and the "r-neg-b" ==> "indie r&b" rename... is the proximity of these genres on the canonical map:
future garage, indie r&b, wonky, and metropolis.  

* indie r&b and wonky are natural partners, but surrounded by seemingly unrelated pop & urban music.
* metropolis is very very close to a lot of future garage, but is hanging out with nintendocore which feels quite distinct.
* and the distinction between indie r&b and future garage for me is probably just how intelligible the vocals are, but otherwise quite similar. SBTRKT and Mount Kimbie both exist in this "post-dubstep" area but are currently split up with quite some distance between 'em.  
 

Anyhow, really appreciate your efforts to provide a modern and evolving taxonomy. Cheers