I guess the strength memory system does combine quite well with the “direct derivation from blueprint” method. You could seed all the strength memories with the numbers derived from the blueprint and then let the system evolve from there. As you say for non-player patches we could just use direct derivation.
In terms of larger patches each of the n microbes needs to remember, say, 50 numbers about each other species. So the memory required is 50*n^2 bits so for 1000 species that’s 50 million or about 6.25 megabytes, so not totally crazy.
In terms of speed it’s very quick because the memories only get updated each time an encounter happens between two microbes. So you are swimming around and you see and A and a B and they fight and A wins, only then will A and B’s memories be updated so that is extremely quick. If you had a lot of microbes on screen then there would be more updating but not even that much as it would only do it when the encounter was over. So I think pretty cheap overall.