That's really funny -- I was just performing an experiment because I'd also noticed the weird tendency for mono-colored populations and wanted to make sure it wasn't a bug!
I divided the level in two with obstacles and sure enough, the two populations diverged pretty quickly. On the left, color diversity took off quickly, going through pink, orange, and yellow before settling on white. On the right, there was very little change for a very long time, with the population staying very close to the original red, before eventually starting to diversify into pinks and purples. So, at least I know that works! The popular colors are just out-breeding the rest.
Some advanced logging would be really neat. I bet you could extract some really cool data! I've been mostly hesitant to add new options to the game simply because of UI clutter -- there's already so much going on in menus. But as the list builds up I think I'm seeing the need for at least a dedicated "Settings/Options" pane. So I will probably look into adding autosaves and logging along with that.
As for the random generator, NeuraQuarium does *not* use a seeded generator -- which means that, yes, when you reload a save, you are going to see a different result.
That's something that could potentially be changed (or even have an option added) but it would require a little more investigation and work. There are a LOT of random events, and pursuing a goal of total "seed determinism" would even require changes to the save/load system, as some level elements (grass/weeds) do not preserve EVERY aspect of themselves -- when you load a save, the grass might be slightly different colors or sizes, because only the location is saved. So, that's not a "no," but it's a "not tomorrow" ;)