In the game's lua files, I notice the following two recipe categories, with the following recipes:
- organic-or-assembling
- Biochamber
- Nutrients from Spoilage
- Nutrients from Fish
- Nutrients from Bitter Egg
- Wood Processing
- organic-or-hand-crafting
- Yumako Processing
- Jellynut Processing
- Copper Bacteria
- Iron Bacteria
- The Engineer/God Controller
- Biochamber
- Assembling Machine 2
- Assembling Machine 3
- There are no other recipes in the game (other than scrap recycling) that can be hand crafted, but not crafted by an assembling machine 1
- All the other 'or-assembling' recipe categories (metallurgy-or-assembling, electronics-or-assembling, and cryogenics-or-assembling) do not allow hand crafting or Assembling Machine 1
- The other 'or-hand-crafting' recipe category (recycling-or-hand-crafting, used solely by scrap recycling) does not allow Assembling Machines, but only the character
- organic-or-assembling to only be made in a Biochamber or Assembling Machine 2 & 3
- organic-or-hand-crafting to only be made in a Biochamber or by the Engineer/God
It doesn't bother me much either way (as long as there's a way to make biochambers and automated nutrients without a biochamber!)
(On a related note, I noticed another pair of duplicate recipe-categories: "basic-crafting" and "advanced-crafting" (they require Assembling Machines 1, 2, or 3), but basic-crafting is unused, and advanced-crafting is only used by Engine Units, I'm guessing 'basic-crafting' was simply not deleted when it was no longer used?)