You misunderstand. MC maintains the metadata (tags) in the database, and then writes them to the file if possible. You don't get rid of metadata in the database (database tags as you call them); the database is how MC functions. If you don't want metadata in a database and want to exist only with file-based tags, give up MC and use Foobar.
When you analyze audio, it is the database that is updated. It will write the updated values to the files at the same time if it can. You can force it do so so (again) later with update tags from library. If the tags in the files are wrong, it will not affect playback in MC.
Fix the writing problem, update tags from library, and then the files and db will be in sync.
You need to focus on the problem whereby MC can't write to the files first, before you pursue your plan for "tag domination ".
I think you also need to gain more experience and understanding as to how MC works with tagging before you can control everything manually.
https://wiki.jriver.com/index.php/TaggingFor example, you said you are using FLAC. Therefore, you don't need sidecar files. Forget about that.
Good luck.