this makes the most sense especially with the lines about how the machines discovered "a form of fusion".

the "batteries" whether purely electrical or chained together into wetware that helps run the Matrix, are basically redundant now that fusion was jumpstarted and they are preserved because the machines were basically communists and only wanted to help (according to the animatrix. remember once pushed into the desert to be isolated in machine gaza they basically created post-scarcity causing all the right wing dominated nations to declare genocide)