Wow! Great project and great write up!
I’m not sure if you’ve seen this or not, but you might be able to set the order of operations using the colors you pick. I’m not sure how it interacts with cuts and engraves, though. Here’s @marmak3261’s post on it.
Custom Inkscape, Illustrator, CorelDraw and Affinity Designer Color Palettes for ordering operations in GFUI