After getting the stacking module, I can no longer handcraft a stone furnace without first doing the manual handcrafting of crushed stone to stone. This mod is preventing this.

It's trying to uncrate the stone instead of handcrafting the crushed stone to stone. Can we add a config or some way to disable handcrafting / uncrafting of crated items.

That's.. very odd. The unstacking recipes have the allow_as_intermediate flag set to false because of exactly this, there's been a bunch of discussion about it over in the forum thread. You didn't happen to make the change that I mentioned in this post in your local copy of your mod, right? (That's what I would expect to cause this) Assuming not.. I hadn't realized the unstacking recipes were actually interfering with handcrafting intermediate items even just being present.

This might be a bug with the base game, I'll do some more digging. If that is the case, I'll get an option added to go back to the 'old way' where the unstacking recipes aren't a category the player is capable of crafting.

We'd not even stacked anything. Just completing the research for the stacking boxes immediately breaks this. For the time with our pack we decided to completely disable the belt boxes.

Can you upload an affected save? I wasn't able to reproduce this issue, even with the tech unlocked it happily crafted absent stone from crushed stone to make a furnace, with both stacked stone (from vanilla) and with or without the stacking of crushed stone from this mod.