This might exist already and I am just bad at finding the exact code I would need to use. But is it possible to (with the use of MineTweaker or similar) to code in custom recipes for some of the machines?

I help develop large modpacks (Project Ozone 2) and we are looking at 1.10.2 mods for PO3, part of that investigation is to see how they work, both standalone and how well they can be configured to work as a part of a larger whole. The idea is to make people use mods they aren't familiar with, or use them in ways they aren't used to. So I dont have any specific ideas at this point, just want to know if its possible.

It is not - but I may be able to support that. What are you looking to use it for?