Especially in more recent versions of MacOS, I am always fearful that cloning will fail to reproduce some of the wrapper-files and fru-fru needed for proper disk structure. This fear is not based on bad experiences, it's just the way I approach it.
So I always install MacOS from scratch, and add my files to it. Since this is a common debugging technique in case of mysterious issues with MacOS, it seems like a good thing to do in general. It gives an uncluttered environment at first run.
It's great that you are serious about backups. But with all drives inside the MacPro chassis, you are sharing one component that could take out everything -- The Mac Pro power supply. Next time you upgrade a drive, consider making one of your backup drives a stand-alone external drive.