Very cool. A few years ago at NFL we built a CMS similar to this for managing sites and apps. It was called Component Builder and similarly you could cobble together pages of components (and deeply nest them however far you wanted) and configure each component and persist the final outcome in a database. The frontend was not open-sourced, but the backend was: https://github.com/nfl/gold
Your project appears to be generating a static SPA, but if you wanted to consider making this a full-fledged CMS you could look into using gold or something similar.
graphql really shines on the CMS side where your Component schemas practically write the cms UI for you. Your cms UI can leverage introspection to make for a really intuitive and efficient experience - especially considering that your atomic component library will grow very large over time.
I like how you split up component types (atoms, layouts, functions) and nest that under the app component types (pages, templates, flows) Is this done in code or are you using proptypes or some schema to manage the organization?