You are correct that there are externalities. But even if we priced in thise externalities, it would most currently NOT 100X the price (which is what would be required to make vertical farming cost competitive).
I would be extremely surprised if those externalities even came close to 2Xing the price of "normal" farming.
Both land use [1] and shipping [2] contribute significant fractions of our society's carbon budget.
[1] http://science.sciencemag.org/content/285/5427/574
[2] https://www.transportenvironment.org/press/shipping-emission...
That said, I'm not so sure about 2-story, LED-lit warehouses for growing food either...