The enzyme system you suggest is interesting but I have a few reservations with it. What is the advantage of this system over using percentages? I feel like it’s a little unnecessary to create a new compound as part of this system. Also how would the game keep track of which Organic Matter was ammonia, which Organic Matter was phosphate, etc.?
Also, I think it’s important that organisms not be able to digest all of the compounds from food they eat. Realistically digestion is never perfectly efficient, and that’s a theme that runs all the way through the Aware Stage as well, where organisms feed on carcasses but only extract some of the nutrients from them. A common chemical benefit of adaptations to the digestive system in biology were that they increased the yield of compounds/nutrients harvested from food.
Also, a concept image of lysosomes for any artists that want to create concepts or models for lysosomes.