In a previous post, I talked about add-on scopes. One of the things that was most problematic about add-on scopes was where the
extensions.autoDisableScopes preference could be set. In my original testing, I thought I was unable to set it in an autoconfig file. I've retested everything in the ESR 17 as well as the current Firefox, and to my surprise, this value can be set fine in an autoconfig file (although not if it is remote).
In addition, for files in the defaults/preference directory, there were issues with JS files only working if the filename started with a letter less than f. That problem appears to not be there anymore either.
So to summarize, you can set extensions.autoDisableScopes via autoconfig (and you should) and it doesn't matter what your JS file in defaults/preferences is named.