So when I optioned for the cobble and deepslate slab crafting quests, I noticed that you have to click the output item manually and no shift bulk crafting. If you shift bulk craft it does not recognise the craft and does not count, not sure if thats an intended feature
This is intended at the moment. I can change it, but for now I'm leaving it and seeing how things go and if I want to change it or not. Changing to count per item crafted over per craft action means a lot of quest requirements will change as well to keep a balance. I'm already thinking about it, cause I can see how annoying it is, especially with the craft actions that only craft x blocks per action, and interfaces like Stonecutter are not counted.
After careful consideration, I've decided to keep the system as pay-per-craft action. Switching to pay-per-item crafted would require significant rebalancing of most quests and crafting jobs, likely leading to reduced income or increased difficulty. Since the current system is working well, it makes sense to stick with it.