First, you're underselling it. 95% less pesticides is huge. If that's economically viable we're a LOT better off. I have my doubts since it's clearly a PR video, but still.
Secondly, the analogy falls short. The goal of horses and cars is transportation of goods and people, which is easy to measure and cost. Agriculture is about utilizing immensely complicated biological systems to deliver nutrition to people. We don't know everything about nutrition, let alone everything that contributes to making nutritious food. That's why we always look for minimal modifications to biological systems in order to tweak it to our liking. The same is true for say medicine; we don't design an artificial organ if we can avoid it, we usually aim for something like a simple chemical compound that triggers an existing response that helps the organ function normally, as defined by our existing biology. We may be quite advanced species, but biology is not exactly something we master.
> vertical self-contained (almost completely closed systems)
Well, sounds more convenient for humans, that's true. But if you take nutrition out of the system you have to replace it with something, which I don't think we've figured out.