What problem does this address?

It would be nice to have a section in theme.json for settings, which are used for kind of 'special user defined' which is not parsed by Gutenberg/WordPress.

Using workflows and build tools (Webpack, Babel, Sass) which could import the 'special user defined' (and of course other settings to) for getting these settings needed to build and compile. With this, a theme developer may be able, to adjust all settings at a centralized file.

I have many settings, which I have to set several times - for sass, javascript and php. Why not use the theme.json as an centralized config file and parse or import it every where it is needed?

What is your proposed solution?

Adding a section to theme.json, which is not automatic parsed, modified or overwritten by WordPress/Gutenberg core. Make these section clear to all developers with a specific name, for example site, sitewide or what ever.