Biosphere 2 had the problem, not least, that it didn't have enough of an atmosphere to buffer swings of CO2 concentration between day and night. It's like "what did they think would happen?"
I think it is more that you need a specific endpoint and a real business plan. Like how could Biosphere 2 have really made money?
A closed loop ecology for, say, survival on Mars, is an interesting question that somebody might need an answer to but there is no reason why it needs to look like the Earth with oceans and all and it might lean heavily on bacteria that live in vats or 24 hour illuminated agriculture or something.
Meanwhile it is not so clear that from a scientific point of view that some experiment in a greenhouse can give conclusive answers about the ecology of the Earth where so much is going on.