When I played the new version, I literally could not tell where my organism was in the dark biomes because the environment in those biomes was so dark. Even when I changed the membrane color or membrane type.
I think it also has to do with what is considered a surface biome. When I was attempting to induce the Snowball Period on a small world, I noticed that the Mesopelagic and Underwater cave biomes underneath an Ice Shelf also need to be oxygenated. Even though those biomes are not located at the surface.
An additional thing, after playing more, I think that the tolerance penalties should be reduced. While I am fine with the new 20% Osmoregulation penalty for each individual tolerance since I play custom difficulty, I am worried about whether the additional tolerance penalties would be too punishing for new/returning players who play on regular difficulties. Maybe reducing the individual tolerance penalty by 25% (making it 15% rather than 20%) would be a happy medium between increasing the tolerance penalty from before and not making it too punishing.