Speaking of base resource inputs, I would be concerned with the soil erosion inherent in intensive farming methods. By every estimate I've seen of the rate of topsoil depletion[0], we'll reach a crisis point in agriculture within half a century. Could vertical farming, perhaps paired with a less pollutative energy source like nuclear power, stave off that eventuality? I know a lot of people push organic farming as the solution, but it doesn't appear to be productive enough to feed a growing global population.
You still have the problem that you need to be able to grow plants beyond lettuce and strawberries. No one is growing cereal grains or root crops vertically. It’s not economical viable.
Quite simply, the energy and capital costs of growing bushel of wheat are more than the bushel price of wheat. This difference isn’t just a little, but a lot. If I’m reading the table right in page 19 of the appendix linked, it’s as bad as 37x in 2019, and only projected to fall to 4.6x by 2050.
[0] https://news.un.org/en/story/2019/12/1052831