I am just having some difficulty understanding the importance of linking to a database if only the settings are stored by the database.
Maybe take a look here and see at least the default info stored in the database:
https://codex.wordpress.org/Database_Description#Table_Details
There is much more there than just theme settings.
Why not just store the settings in the WordPress install itself with everything else?
I suspect security might be at least part of the answer there in relation to many things, but theme settings are likely stored in the database in order to isolate-protect them from being overwritten during a theme delete-and-replace update.