I'm sorry, but I had to reply to this topic. Especially since most of it makes no sense.
There are no side effects. Please try to understand what 2-way sync means.
Joplin is not a markdown editor, but a note-taking application with markdown support. Your use case has nothing to do with Joplin.
I have no idea what you are trying to say. Joplin does not have to sync. If you want to sync, you can use WebDAV, Dropbox, Nextcloud, or a local filesystem.
You want to use Joplin to edit your local files. Joplin wants to be a note taking application. You are not supposed to touch any of the files that Joplin creates - neither locally nor on the sync target.
Also, as mentioned earlier, Joplin is not a markdown editor.