All of your questions are about @Solo0815 diff script. I don't use it or snapraid. So, I will try to answer the best I can. Everything done in Windows should work on the plugin. I refer to the snapraid manual a lot when working on this plugin.
It is automatic once you start it. So, you just need to start it at boot.
Scrub frequency is how often it runs since the script is always run. It is meant to be a scrub because you don't need a script to run sync. sync can be done with a scheduled job. All of the paraments in the diff script frame are used in the script and nowhere else. The settings are defaulted to whatever solo0815 uses.
Scrub percentage is the -p parameter. Once again, it is just a default. Maybe solo isn't using it on large files so it is fast.