Yeah, good question. Apparently in the early drafts of the Matrix, they used human brains for their computing power (you can still see a similar idea in the short story Goliath), and the Matrix was just to distract the humans while this happened. it's said that Hollywood executives thought that this was considered too confusing back in 1999, so the Wachowskis used the "human battery" idea to try to explain why the Machines still needed humanity.
I wish they stuck with the bio-cpu part, the whole human battery thing is just, completely impractical. It would take much more energy to keep everyone alive than what they'd get out of them.
I was never able to track the source of the "bio-cpu" or neural processing script change rumor myself. It always made sense, and Goliath is perhaps my second favorite matrix comic, and I agree this may have been one of the only concept battles that the Wachowski's lost with the studio on the project. I've just never been able to verify it, if you know where the information originated and can share the roots with me I would be very grateful.
Meantime, I made a whole video on this subject:
I believe that if you take a close look at some very specific details of the Animatrix, The Architects speech, Morpheus explaining that the dead are recycled, present body heat technology, and the actual laws of theormodynamics, the concept of a human battery is not anywhere near as problematic as they suggest in futurama. More specific to the OP, my interpretation is that the "human battery simulation" is a prison industrial complex solution. The machines never wanted to destroy mankind. The Animatrix goes over the history of the man vs machine war, and the machines wanted peace. The machines never wanted to exterminate humans. They simply wanted to avoid their own extermination.