It is nice to know you like the idea :D
I think most of it are good idea! I will definitely add water into the mix and make it consume 2 carbon stead of just 1, despite it will still have a possibility that someone will bring it to vulcanus and get exploited, but it is more fun to have such interplanetary strategy.
And I should mention, Biosynthesis Recipe do have a problem, If recipe stoped because you have too much coal or crude oil, carbon bactetia will just evaporated and you have to import them again from your loop or even request import.
The problem of yielding more bactetia is that those oil-making and aquilo recipe don't use nutrients in their machine and recipe, even if it did it be too much challenge to normal factorio player, it id already tons of player just skip the Gleba and only do the bare minimum; And I already allow them to duplicate if you use biochamber to refresh the carbon bactetia, despite you cannot put prod module in furnace, you do gain more carbon bactetia with Biochamber's +50% prod boost; but I think I can implement it in bioflux related recipe tho, How about make it create 10 bacteria instead of just 2? And carbon bactetia will even just solved itself by disappearing.
I will think about nutrients out of thrust fuel, tho I should mention this mod's dependancy "cooking_nutrients" already make burnt-spoilage carbon require yumash (Yumako Mash).
As for Aquilo and Boompuff, well maybe ;)