From your question, I assume that you believe that Zion and the world around is the real world. The reason why there are so many inconsistencies regarding this world, for example :
- The point you raise
- No cataclismic climate change (nuclear winter and/or greenhouse effect)
- The weird use of something as inefficient as human heat as an energy source
- Neo having powers
is that it's a part of the Matrix.
Most characters of the movie believe (at least in the begining) that they are in the real world. The spectator also believes it at some point, but only because Morpheus states it as a fact during a scene where he explains the plot.
On the other hand, the Architect explains that the Choosen One's purpose is to reboot the Matrix, rebooting Zion in the process. How could it be possible if Zion was out of the Matrix.
Also, the whole trilogy revolves around the Illusion of Choice. It's te innovation added to the Matrix which stabilizes the humans in it. About that, the Architect declares that the perfect world Matrix was a disaster until they added options : the humans needed to have at least the impression of having a choice.
That choice is Zion : The humans that are the most prone to contest the reality around them will be met with the choice between staying in the Matrix or escaping it. While that choice makes no difference, it makes them cope with reality : they believe they are out.
This idea become even more obvious if you take into account that the Matrix is inspired by 1984.
In this novel, the main character grows doubt regarding Big Brother and joins the clandestine opposition, spending the rest of the story fighting the wall of lies set by the government from the outside. The final twist of the novel is that the book that inspired the opposition was written by Big Brother for that exact purpose. The idea is that when you aim for control, the best way to have no opposition growing is to create and control it yourself. That way, it's an additional layer of control in which the free thinkers will live in an illusion of contestation.
The point being : Zion has not to be realistic. It has to be believable. The dialog about how chicken tastes and what the Matrix knows about it is very relevant in that regard : The characters figure chicken's taste from their experience in the Matrix and admit that they don't know for sure if it tastes the same in the real world. We can add that for as far as they know, maybe chickens don't even exist. So the fact that Zion is flawed is relevant, since they have no real world to compare.