The thing is that if players are just able to keep adding mitochondria or other ATP generating parts endlessly, then there is no real reason to take specialization and adjacency very seriously. Why worry about making toxisomes, flagellum, mucosysts, etc. run more efficiently if you can just place however many number of mitochondria to produce that extra energy surplus?
Optimization-focused mechanics work because there are constraints that the player faces. If there are no constraints on the player, then there is no reason to work with what you’ve got - you can always just add more to solve whatever design problem you face. When it comes to the multicellular stage, we don’t want to have the same editor process and dynamic of the Microbe Stage, where growing isn’t much of an issue.
That could get really stale; especially in a stage where the focus is really optimizing and fine-tuning your creation.