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.
That is not how Arkenfox works. You apply the patch using the script, and then re-run this patch everytime Arkenfox receives an update. In between running, you can change settings in about:config and settings, but it will be overwritten if a different value is included in the user.js. A more permanent solution is using the user-overrides.js file required by the script before patching to create a persistent config.
I know this is somewhat defeating of the privacy purpose but I use FF because of sync- is there an alternative that can use something like webdav to sync my bookmarks/history/etc between instances?
e; i know floccus is around for bookmarks but i find history useful too
I really doubt they would care about something like this. Even getting them to support firefox was an annoying process. I emailed them every month for six months until they added firefox support
This is expected if you keep the default settings. You shouldn't use it as it is but read the wiki and configure it to find the balance you want between privacy and usablity.