Its better to just go through the settings yourself then rely on arkenfox. This just adds a middleman into the process of keeping your settings updated.
Have you seen the user.js, you have to change a lot of settings and you cannot keep up to date with them, secondly Arkenfox prefers you to go over their user.js by your self and their updater script has the -c flag to show you the difference between current user.js and new user.js
Overall it would be very difficult to manage something like this on our own as most things are not visible on the settings page of Firefox
In addition, if you use user.js then you essentially cannot change those settings at runtime (via about:config or otherwise), because your user.js will override the settings on next startup. Maybe that's desired for some, but good to keep in mind nonetheless.
I don't think that could work. Not unless we are talking about different things, or unless you run their updater script everytime before starting Firefox.
If you use user-overrides.js, it adds your custom preferences at the bottom of the user.js, as the prefs are read from top to bottom, if a new duplicate exist in your user-overrides.js but with a different value the new value would be used as it is at the bottom.
Yes, but that is not what I'm talking about. What I mean is that when Firefox is running and you go to change some setting in say, Settings page, then the new value for that preference is stored into prefs.js (at latest on Firefox shutdown, it might remain only in-memory for some time I'm not sure). Anyway, the new value persists only for that browser session, because on next startup whatever value was set by user.js will override it.