While this mod is enabled in mod settings, Crafting Tools and Handy Hands (Refactored) will stop crafting after running out of intermediates :D. Crafting Tools can be forced to make the intermediates by pressing one of its hotkeys a second time.

It might be worth noting that this mod was never really intended to be used with other handcrafting mods (it was made on request for a reddit user, for whom this is their only mod).

Crafting Tools' behavior is pretty much what I'd intend to happen anyway, had I accounted for it. Handy Hands I'm less sure of. I'll look into it, I guess.