As it stands, Quantum Fabricator requires the recipes it uses to have a 100% chance of success. Scrappy Industry changes nearly every recipe to not have a 100% chance of success. As a result, only a 7 entries in the logistics tab were accepted as valid, 5 of which it won't even craft anyways because they're tiles. This essentially makes the crafting component of Quantum Fabricator useless. There is an option in Scrappy Industry to ensure that recipes always succeed, but it's not the default.
Attempting to fix this would require some logic to deduct a random amount of materials when attempting to craft something, which could be tricky to get right.
From the looks of things, byproducts are handled, though if they're only used in recipes for intermediates, they'd be difficult to use prior to getting the dedigitizer.