You should think about adding catalyst_amount to your calculations. This recipe product property, added in 0.17, lets mod authors make some of a recipe's products immune to productivity modules. The new formula for product rate is something like:
amount + (amount - catalyst_amount) * productivity

https://wiki.factorio.com/Types/ItemProductPrototype#catalyst_amount
https://wiki.factorio.com/Types/FluidProductPrototype#catalyst_amount

Can you point me to a mod/recipe that uses catalyst_amount? Thanks!

Actually, the base game automatically sets catalyst_amount for any recipe whose ingredients and products overlap. If you inspect the products of kovarex-enrichment-process inside the game, for example, you'll see that "uranium-235" has a catalyst_amount of 40 and "uranium-238" has a catalyst_amount of 2.

Ah, I see! I'm testing now with a koverex setup with Creative Mod, and the numbers were very wrong before I changed the formula per your suggestion. I'll release a fix after some more testing

See version 3.2.23

Thanks! By the way, are you planning on fixing the mining-drill calculations soon?

mining drill calcs are now back, as of 3.4.37