Great work, it's all coming together nicely.
On the question you asked about compounds locked, if that's the system we end up with, the way it works is continuous. So basically your species is like a sack and you have 1,000,000 protein and you lock away 10% per minute (or whatever) and so, after a while you have 500,000 free and 500,000 locked. It's representing thousands or even millions of individuals being born and growing, but because that happens so smoothly we can call it continuous.
Then over time you also lose, say, 10% of your compounds locked per minute. That way there is a steady flow from your compounds locked pool back into the environment. This represents members of your species dying.
Finally your species absorbs compounds from the environment into it's free pool. So there is this continual flow
environment - [absorbed through membrane] -> free pool - [growth] -> locked pool - [death] -> environment.
Does that make sense? Basically so many of these actions are happening that it looks like a smooth flow. Individually it's single microbes being born and growing and dying in sudden shocks but with so many happening it looks smooth.
Also your point about infinite water is a good one. Given energy over time it could cause problems.
Overall interesting. As you say above I am most interested in the person who builds this having ownership of it. Whoever they end up being I'd love to help them as much as I can in any way. However until then I'm not sure I'm helping.