> I have this intuition that the borrow checker might enforce a way of working that fundamentally stops you from doing things that aren't _really_ compatible with the way a CPU actually works on the lowest level.

No, I think you are reading too much into it. One is free to Box-allocate/pointer-chase on every line in Rust without any trouble. Sure, as other low level languages, rust also prefers/makes stack-allocation more ergonomic/the default, which is a quite cache-friendly way of operation but not even the stack is “native” in and of itself - it is just a frequently and extensively used part of the “heap”.