Well if you use antibodies, they should be able to slowly be excreted and broken down after a while. I don’t believe antibodies undergo any memory effect. If you use a specific form of T cells, they should undergo the same degradation, although I guess there is a possibility that in some unknown cases it might revert to a memory cell, although to my knowledge this doesn’t happen. Lastly, since the virus used to express the receptor should only infect the cells extracted from his blood, any autoimmune response shouldn’t last (since cytotoxic T cells don’t last forever). The virus isn’t self replicating, and isn’t used to infect any other cells.
I don’t believe you have a compelling argument, any biological organism has a degree of unpredictability, but with a series of molecular checks and controls, it becomes predictable, almost deterministic. Think of how the brain works, how you have billions of cells acting the way they “should”, and acting in a predictable way allowing you to perform daily tasks. I agree we have a lot to learn and that some mistakes might be made, but that’s what testing and clinical trials is for.
