Perhaps I'm reading too far into what you wrote, but I'm not sure I agree that the CPU is fundamentally different from other layers of abstraction in computer systems.
All abstractions “lie” in the sense that they present a perspective of the world that is slightly different to the reality — function calls “lie” about the operations that are really being performed, the ISA “lies” about the electronics of the CPU, and transistors “lie” about the underlying behaviour of the universe.
All abstractions “lie” in the sense that they present a perspective of the world that is slightly different to the reality — function calls “lie” about the operations that are really being performed, the ISA “lies” about the electronics of the CPU, and transistors “lie” about the underlying behaviour of the universe.