This is exactly the point the author is arguing. The focus of all their work on UB is to make sure safe Rust can do all the optimizations we would like, by careful design of the abstract machine.
The immediately visible outcome of this work is a set of rules for what you can do in unsafe Rust, which taken together amount to this weird-looking abstract machine with its extra "uninitialized" values- something that can be implemented efficiently on real hardware assuming no UB.
The point here is that this abstract machine is a better, simpler, easier way to convince yourself whether or not an unsafe Rust program is well-defined, and that "what the hardware does" is too many layers removed to be a good tool here. You can think about "what the hardware does" another time, for other purposes, but trying to do so in this context is actively unhelpful.