The title ^.
Would be great if my Flawless(!!) gear wheels don't look like a series of marigold flowers on a belt.

Most probably a suggestion for a new mod

Customizable how? From a preset of icons or by bringing your own images? If you have your own images, a mod wouldn't be able to read them, but you can just replace the icons in your game files.

Oh, seems I missed your reply for almost a month! Sorry about that..

My suggestion was preset icons. Probably one alternate set only to start with is good. Something that is more apt to the idea of "quality" of materials.

Quick question: Does the API allow for changing the shade / apply an overlay to an item, or would that have to generated in data stage for all quality variants? Ideally, I'm thinking the item sprites become shinier as quality increases (complementary to icons or with an option to disable icons altogether). Could be more immersive that way

You can tint items with a shade, but different qualities of the same item is still the same item, you wouldn't be able to tint them differently sadly.