A silicon atom is 0.2 nanometers and the smallest single transistors used in recent chips is in the order of 5-10 nanometers.
Also, using photons instead of electrons does allow you, almost literally to handwave away he size of atoms. How exactly, is unknown today.
Photons at usable frequencies are much larger than atoms. Just notice that lithography is currently moving into what they call "extreme UV" (and most people call X-rays) because the UV photons are much larger than the features of current top of line chips.
Is that a fundamental theoretical limit like the uncertainty principles or is it a matter of engineering advancements to figure out how these forces work? I can imagine carefully positioning two atoms (maybe moving?) to obtain similar effects.
Jevons Paradox is not an immutable natural law. It's does not even have any predictive power. It's just a notice of an interesting thing that can happen but the naivest interpretation of microeconomics assumes it's impossible.