https://imgur.com/iale5oN

When I try to handcraft something, it always picks the unstack recipe to make the ingredients , even with the uncrafting recipes hidden for the player character

That really shouldn't be possible, unless you've applied a local hack to your mod of the allow_as_intermediate flag that I described way back in this post, or another mod's messing with something. It's working fine for me, can you upload an example save somewhere so that I can sync my mods to it and track down what the heck is doing this?

sure, here ya go
https://www.dropbox.com/s/p8ogdwrzoxac5b8/WW3.zip?dl=0
As for mod conflicts, the only thing that I know of that could probably mess up smth with inventory recipes would be the crafting efficiency mod