Ahhh, shift clicking the item out of the crafting table doesn't work while editing the result through the event. This is a problem with the Container#mergeItemStack because it uses ItemStack#copy and places that into the new slot or just modifies the current slot with a matching item. This can be 'fixed' by overriding the Items using substitution, using the Right Click/Player Tick, or whenever the vanilla ContainerWorkbench opens replace it with your own version that overrides the mergeItemStack method and applies the data to the stack when it comes out of the result slot or even using a custom Slot for the result instead of the vanilla one which will allow you to modify the Stack any way you want.