Would it make sense to have the ability to create post type templates first? For that we would need placeholders for title, featured image, content, post meta fields, comments, tax terms, related posts, read more, and navigation blocks for singe and archive. Toolset Blocks has this now, which might provide an example. It doesn't use HTML templates.

There are also a couple of themes with header and footer builders, like Blocksy, that might provide an example here.

And the latest Elementor beta added some global styling options which might also provide some ideas.

Perhaps the Customizer would be a place where you have a page or set of pages with content like the theme unit test data where you could set global style options for buttons, tables, quotes, etc.? Or override the theme's defaults.

Will block-based theme's have hooks for replacing the theme's default header and footer? Or will the theme have block areas like we currently have widget areas?