By the time of Neo, the Matrix itself functions as an afterlife for adaptive programs whose functions no longer exist. To do away with the matrix is to risk more aberrant programs like Smith when no secondary option exists for program with no purpose.

None of the scientific understanding in the books/movies/cartoons make any sense. Any form of fusion makes batteries, bodies, humans obsolete. EMP devices being localized to massive ships. Robots who already built the greatest city civilization had ever seen, couldn’t build above an arbitrary cloud point, much less catapult themselves into orbit or to other planets. Everything is wrong to the point that the inhabitants of Zion could theoretically be in a different matrix, potentially programs themselves.

There is a point in the Animatrix where after the machines win the great war and humanity signs the end to the war treaty, the ambassador of the machine world encloses an apple and there is a nuclear flash. I took the imagery and the flesh quote to mean humanity wasn’t used as batteries so much as the machines took whatever transformative code base for humanity into a cold storage form then ended the threat forever through nuclear flash. Even before the end of the great war, the machines had generated contagions to the point that humanity was doomed anyways. The matrix being a story, within a story, within a story. Neo being an emergent truth of the creators, that there was value in philosophical concepts beyond just material understanding that might be being tested out by a more advanced form of sentience. Same way we might try to impute deep meaning from some scrap of parchment or wall scratches.