Yeah these are really nice ideas.
For the microbe stage we are already working on having membrane bound organelles locked until you have a nucleus to reflect the symbiotic origins, though we could do more. The predator prey relationship you talk about could be a microbe thing too, such as small ammonia producing bacteria which hang around large photosynthesizers, that would be interesting.
Re society you could argue that civilisation is a symbiotic relationship between many species. Plants (wheat, rice, fruits and vegetables etc), animals (horse, cow, pig, dog, elephant etc) and humans all working together and sharing resources.
Re having two sentient species that kind of happened in Earth’s history, there were Homo Sapiens, Neanderthals and Denisovians and more alive at the same time, they interbred and competed to become what we have now. It’s not such a stretch that if the Americas had become cut off earlier they could have been discovered to be full of Neanderthals, which would have been a crazy discovery!
Cool ideas, symbiosis is a great theme for Thrive.