You can stay at the version of clover you are using now for future updates of Mojave. Every update should install no problem. Catalina requires some trickery to get going on unRAID right now because we need at least 4900+ version of clover to get it to install.
As for your app store issues it can be a little janky at first login but for me I was logged in without issue after that. I know changing certain things in your clover config will make the apple account log out and you have to log in again. Also make sure you aren't using a serial number for your machine that's for a actual Mac, make sure it's clean.