Who said anything about eliminating all large-scale rural farms? (And FWIW what I imagine would still very much be commercial farming)

Even barring any future innovation in city planning (better distribution of sunlight, etc), architecture (tiered building design, whatever), and agriculture (crops optimized for greenhouses), we would still benefit from growing food on rooftops, so why wouldn't we?

Oh and by the way, you can use electricity (realistically from a mix of renewable and nuclear power) to keep "sunlight" on in your greenhouses; they don't need to be on rooftops.

I don't disagree that it doesn't scale vertically nearly as obviously as it does horizontally, but why make perfect be the enemy of better?