Yes, I guess that is true. If the parent has a mass of X and then has an offspring and afterwards both the parent and offspring have a mass of X/2 then the total amount of compounds in the species has not changed. We’re not keeping track of any individuals or anything like that, just the blueprint/genetics of the species and the amount of compounds they are holding in total.
I think the plan when it comes to relating the swimming around with the CPA model is that the swimming around will have no effect on the underlying CPA (if you kill 10 out of 1,000,000 members of a species in your patch that is closer to 0 than anything) however what you experience as you swim around is slaved to the CPA. So if the CPA says your biggest predator is species Y and they outnumber you 50 to 1 then as you swim around you will see 50 of species Y for every one of your own species you meet.
The idea behind this is that when you mutate your creature in the editor you will have to optimise for two things, 1) While swimming around what organelles do I want and 2) in the CPA how can I help my species the most. If the swimming around is slaved to the CPA tightly enough, and the CPA models the swimming around well enough then these two problems should be the same. Ie if you add a flagella and that makes you better able to flee your predators then also your species does better in the CPA for the same reason.
However this is a super complex problem so we’re going to have to wait for some programmers who want to work on it and then let them build what they can and then accept that. I don’t want to get too pie in the sky about it, you could easily do a PhD on this problem (many people do, modelling microbial interactions, for example).