I wouldn’t recommend physical copies of the files. I think mysqldump is smart enough to capture a consistent snapshot of the database and, importantly, is still restorable if the server decides to upgrade MySQL (I speak from experience!). The commands you show look about right but I can’t test as I don’t use MySQL for Kodi.
It’s a good idea to stop mediacenter anyway on the off-chance something gets written to the database while backing up. You’ve reminded me to add it to my backup script.
Physical copies have the benefit of simplicity, which is important in a domestic-use environment. And when it comes to restoring data, there are no unpleasant surprises, like oops, did I forget that option? Journalling is all fine and dandy but we’re not talking about a 24x7 system here. I’ll stick with KISS.
Well maybe I’ve missed something, but I’d be hard pressed to tell the OP exactly which files to back up and how to restore following a mysql re-installation. OTOH mysqldump is well documented.