This is a minor nit, but I find that app.config is usually filled with things which might be set from an external config.py file, environment variable, or some other source. I often even like to be able to render these things back to e.g. JSON to save the current configuration for debugging.
OTOH, flask provides app.extensions as a specific place for extensions to store state, and many flask extensions do that (e.g. Flask-SQLAlchemy).
What do you think about having svcs store the Registry object (which is managed by svcs, and wouldn't make much sense to set as the end user) in app.extensions?