Demo of the separated Ink & Paint layers. The ink is against white here (the ink alone is a transparent overlay). The composite shown here is the pre-composite output, generated in the initial render process.

I'm still considering how I want to organizing the compositing stage. Ideally, I want separate access to the ink and paint layers for touch-up work (i.e. to matte out bad lines, add new ones with Grease Pencil, and similarly to make corrections to the paint layer).

Masks (which are basically "traveling mattes" can be used as nodes in compositing. I know very little about Grease Pencil, so it's time to learn!