There will be farmers who will want to perpetuate a distinction just as you have microbrew vs craft vs "commercial" brewers.
Once a majority of produce and fruit can be classified as organic from a chemicals PoV labor intensity may become a point of distinction in order to fetch a better price in the marketplace (I say that as someone who typically supports /buys/ organics).
I guess I don't understand the distinction you're talking about. Are you saying that people would be inclined to pay more for food they knew had more human hands involved in it?
It's a bizarre future, but I guess we're already seeing people pay 25x for a hand bag if they know it was made in a conflict-free village or something of that nature. I suppose its only natural that our abundance will begin to allow us to start making those sorts of luxury designations for our food as well.
It's exactly that distinction I'm making. Oftentimes automated machinery is better at making things than humans at making the same (furniture, cars, shoes, etc.) but people like buying "crafted" items for various reasons (vanity, support of craftspeople, local economy, what-have-you).
However, the main point is some farmers will find some kind of marketable distinction bigger operations won't be able to leverage (labor intensity or small production varietals "heirloom", etc.) Something which would allow them to fetch a better price and make them viable as a business)
I expect freshness and taste/heritage to be a greater selling point than pure labor intensity. A megafarm halfway across the country may use equal cultural practices, but the produce can't be as fresh as the farm just a bike ride away, and for many crops freshness translates to flavor.
Moreover, a megafarm would like to grow the latest and greatest in crop genetics, bred for standard beauty. Small farms are better able to grow the varieties that have been around decades, taste better, and are less perfect and ship poorly or are only exciting to a few people. Or, small farms can grow the newest small-breeder varieties bred for flavor or amazing exotic looks: I'm a big fan of Wild Boar Farms' new tomato introductions, but most people would never buy a mostly-black or an outrageously striped tomato.
You have a point with "heirloom" varieties which will not get the attention from large-scale farming.
The freshness point, I would contend that vertical urban/sub-urban farming could potentially deliver better with regard to some fresh produce and some fresh fruit/berries --not all, obviously, but many of the best selling items --better because they can grow more with more uniform product. The qualifier is potentially, if economics work out.
Obviously harvests which require large trees are out of the question --you can't commercially grow a mango grove or apple orchard in a vertical farm.
Once a majority of produce and fruit can be classified as organic from a chemicals PoV labor intensity may become a point of distinction in order to fetch a better price in the marketplace (I say that as someone who typically supports /buys/ organics).