That only includes the ebuilds, which are instructions for how to build from source, not the sources themselves.

So the sources for, say, Paint or Edge are versioned within the Windows repository?

Yes, most of the components and files in a default Windows installation are built from sources in the main Windows OS git repo.

Some parts of Windows have split out into their own repos and CI build and test pipelines, but splitting is a process that takes people's time and has pros and cons, especially when changes in the main OS repo are needed to give the separated components a complete, coherent API surface.