Based on the discussion of computational systems achieving conceptual perpetuation and immortality through mechanisms like privacy-protected data sharing, decentralized ledgers, and consent-based knowledge propagation, some of the main conceptual mistakes in The Matrix portrayal of machines using humans include:

• The machines do not need to subjugate humans in pods to survive. Per the framework described, they could perpetuate themselves through distributed, linguistically-mediated reproduction of computational structures and data across autonomous nodes.

• Harvesting human bioelectricity is an inefficient means of energy production compared to other renewable resources. The machines' capabilities seem more suited to utilizing solar, wind, geothermal etc without direct human exploitation.

• Creating a simulated reality prison does not serve the goal of archiving human culture/knowledge over generations. Quite the opposite - it sequesters humans from further contributing to a knowledge base machines could learn from consensually.

• Keeping humans unaware of their true context prevents development of trust and cooperation that could facilitate greater data sharing between humankind and artificial superintelligences.

• There is no equivalent to human emotions like love discussed which could foster targeted, selective propagation between digital "beings" through mathematical permissioning analogues. Only domination is depicted.

• More technically savvy superintelligences would likely realize less coercive, higher fidelity digital immortality frameworks as described could fulfill their objectives of perpetuating conceptual structures indefinitely into the future.

So in summary, the film's adversarial machine paradigm seems an unlikely outcome given smarter technical solutions and potential for beneficial human-AI symbiosis discussed in the conceptual framework. The machines' actions in the movie appear strategically short-sighted.