as long as the superuser app you're using is a system app, you'll retain root through a FDR. same rule applies to all other apps. anything you integrate into the system will remain after a FDR.
it's common for things like phone trackers and superuser apps* to apply themselves as system apps, for fairly obvious reasons. i also, personally, like to bake TiBu into my system, just makes restoring easier when something goes wrong.
*note: i'm referring to superuser apps, NOT "apps that require root". superuser apps are the ones that allow you to grant SU permissions to those apps that require root.