Instead of configuring a repository in the repo settings which then get stored in a database (here, atproto), use a special folder, .tangled/, for everything.
Like GitHub is doing it for code owners, funding, and workflows. Just expanding that to all other possible options.
There still could be a settings UI which then would just create a commit to the repo's primary branch (may it be main, master, or how ever it's called).
While I agree that configuration in repo would be handy, it should not be
.tangled/. Instead I think it should be something like.config/tangled. Please, do not pollute the repository root more than it is done right now.