I agree with you, but on the flip-side there's the problem of those who update their submodules via Vundle or Pathogen and all of a sudden have a ton of extra noise added to their dev environment. Those people would then have to spend extra time figuring out how to turn off the extra highlighting which is a PITA.

I'm not against change (or this diff), this is just a bit radical; so I'd like to explore how this looks on popular syntax highlighters.