If you lock the recipe for the autocrafter, it won't use the last item, thus preserving the recipe. But this means unstackable items like water buckets, knives, or Croptopia food tools, can't be used in recipes. I've tried putting extra items in adjacent chests, or trying to pipe extra items in, but the recipe just won't proceed.

That is a known limitation, and unfortunately I don't think that there is a good fix.

for recipes with up to 3 ingredients + 1 unstackable this is still doable via configurations and not locking the recipe
up to 4 + 1 if you manually remove the results (a stack of them, not the single unstackable remainder)
up to 5 + 1 if you don't give energy, but that is probably a bad call