As to using humans for energy, think of it this way: energy is being lost, yes, and fuel has to be used to support the humans, but maybe they are using fuel that is otherwise useless to support the people. Ie, net energy in the system goes down, but energy usable by machines goes up. Of course, what fuel they would have that the most efficient use would be feed it to humans to use their body heat i don't know.

The matrix within a matrix solves all of this, because then the machines are just the construct of some other controlling entity designed to give people something to fight against and oppose being controlled, with a purpose unknown. Not that i necessarily favor that interpretation...