Best way to store per-vault plugin data that syncs?

saveData writes into the plugin folder, which some people exclude from sync. Is there a recommended place for data that should travel with the vault?

I keep user content (not settings) as a normal markdown or JSON file in the vault, in a folder the user chooses. It syncs, it's visible, and people can back it up.

Agree. Settings in saveData, content in the vault.