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. 