Nevermind. I figured it out.
For future reference the syntax file is in /opt/sublime_text/Packages/Scala.sublime-package which is a zip file.
So you need to copy that file and unzip it, change the Scala.tmLanguage file as per the instructions above and then rezip the whole thing and replace /opt/sublime_text/Packages/Scala.sublime-package with that zip file instead.
It's a bit surprising that this hasn't been fixed in the official version. I'll send in a feature request and point this out.
UPDATE: feedback sent (sublimetext.userecho.com/topic/4 ... -included/)