Good points listed here.
Regarding germ layers; I actually find myself coming to a different conclusion regarding their universality, as even complex plants have 3 “layers” of cells (dermal, ground, vascular). I put layers in quotations because unlike animals, plant embryos don’t fold in on themselves, and these differentiated layers continue to develop heavily throughout the plants entire life cycle rather than primarily as an embryo Chapter 12A. Plant Development
A brief google search tells me than fungus development doesn’t feature the same level of cell differentiation, but for complex multicellular organisms, I would assume atleast some analogue to germ layers is needed to meaningfully differentiate cells.
As to their implementation in Thrive, I would think their only purpose would essentially be a way to pace out progression. I think they would essentially just serve to make sure we don’t see an incredibly rapid jump in complexity from simple jelly blobs floating in the ocean to an organism with a fully developed skeleton in just 3 generations. So I would think they would just be a sciencey way for us to justify slowing down game’s pace a bit when a player gets to macroscopic.
Atleast from my memory, there hasn’t been much discussion about the transition to macroscopic gameplay since that initial idea of a mesoglea glob. It seems the biggest difference between that and what I detailed was that for this newer concept, the digestive tract would be formed as you made that jump. I certainly would like a very seamless jump, but I worry about how much we would be asking of the player to form their digestive tract from piecing cells together. Of course however, we could make it as simple as a sort of upgrade however, and that’s what can introduce cell differentiation. It definitely is something to consider.