Farming has the issue of mass scale, as any other human activity. Farmers have been artificially selecting species for thousands of years, but perhaps not at the scale and speed we witness today.
I have no doubts that normalization and lack of diversity are a problem. It is being observed today, for example, in the decreasing quality of tomatoes, that have lost flavour in favour of appearance.
But normalization of food production often goes in hand with normalization of feeding habits, and that is a whole different problem.
For example, potato producers know that washing potatoes decreases shelf life, but they still do it because otherwise consumers wouldn't buy them.
Modern convenience has a lot to do with this, and I think that the solution lies with consumer habits as well. I am all in favour of a more conscientious approach in the consumer-side, but this should be done without resorting to simplifications and emotional responses. It will also take some time.
On the other hand, convenience is a rather early feature of our lives, so I hope adapting to new ways of producing and consuming could be at least half as quick.
In the end, I hope we will be able to use land efficiently, respecting biodiversity and allowing for a reasonable amount of natural harm, without sacrificing quality and, more importantly, food security.
As for Integrated Farming, the Wikipedia article is not as thorough as the Organic Farming article, perhaps because IF is still not a thing in the US.[1]
Integrated Farming is an extension of Integrated Pest Management, Soil management and Efficient Water Usage practices, along with other schemes. It was largely subsidized in the EU for farmers wanting to adapt their methods. From 2020 onwards, it will become the standard for EU farming practices and subsidies will stop, as far as I know.
Integrated Farming is certified by local agencies, in the same way organic farming is: checking farming logs, pesticide invoices, warehouses, equipments and such. A local agent visits my farm every year.
[1]https://en.wikipedia.org/wiki/Integrated_farming