It emulates and enforces that separation. A mathematical abstraction of a Harvard architecture machine has that separation, the real machine merely emulates it, and is only able to do so within some specific constraints (such as: no one hooks up dedicated programmer to the chip, or no one undervolts or overheats the cheap in clever way, or no one takes a swing at it with an x-ray source, or...).

That's the other thing people forget here: we're emulating abstract mathematical universes with real atoms, and then we're stacking those abstractions within abstractions. There is a whole segment of computer security that deals with that. When we say "once attacker has physical access, it's game over", or even discuss "side channels", is when we briefly remember that computer systems live in physical world, and the rules of our carefully designed abstract universes don't hold when you're on the outside of them and reaching in.