The biggest problem with user.js is the documentation, or rather lack thereof. Instead, mozilla should provide full documentation on how this file works and mainly which fuctions are available (FULL LIST) and what they do. In general, the config in firefox is a hot mess and user.js is not the problem.
I think it’s just pref/user_pref and such. Despite the name it is not a js file and is not parsed like one. I think the file extension is entirely vestigial.
But still, there's no complete list of these and only some of them are properly documented. I've tried to look up some prefs about half a year ago and couldn't find it anywhere. There's just a wiki that mentions some of them and on various blogs you can find a mention of what something does here and there, but that's about it.
