Nice job again!
I personally liked this idea:
“Another solution is to have reproductase transfer the compounds over. In essence, this would involve using reproductase as a label for stored compounds needed to produce offspring. Compounds could be converted to reproductase, and eventually released on death and digestion. This does raise further questions though. If organelles have a set makeup, does an organelle-heavy cell need more reproductase to divide? If more organelles are added as a mutation, where do the required stores for them come from if not thin air?”
In nature, bigger cells take longer to divide and move slower. Having reproductase be the amount of compounds necessary for a cell to split in two gives it an actual scientific meaning rather than simply it being a magical molecule that no-one can understand how it works (add reddit and the old forums are prime examples of this fact).
As for your second question, the organelles you add in the editor could already be factored into reproducase’s cost. By this, I mean that you already have a set amount of mutation points in the editor; assuming the player will always use as much of it as they can, we can multiply 100 by the average amount of compounds an organelle requires. Sometimes the player will put in compounds above this average, sometimes below, but if the player goes in the editor often enough the required stores will balance out—sometimes they will dissapear into thin air, other times they will come out of thin air. Does this make sense?