I've noticed in a few places like "New Life" I can knock down stalactites to remove the Hydrons and plant Halids in their place to raise the Biomass even higher beyond what I need to leave the room. But then, why would I do that?

There is benefit to higher biomass than just enough to leave the room. You will need more than the minimum to beat the game but not necessarily everywhere, just enough more to do certain things (trying not to spoil it too much). That said, you will never need more than enough to fill the 5th star. Any above and beyond that is completely unnecessary.

Just finished version 2.0.0. Seems like biomass requirements for each ending have been rebalanced in that for one of them you will need biomass maxed out for all but one/two larger caverns. That does feel like a drag though, only few caverns are unique so wouldn't mind if some of the generic ones would be dropped.