But you choose the trade routes individually. Its not natural, that's the player's choice in where the roads go (except for Rome: all roads lead to Rome lol (special power where every city auto-builds a road to Rome in the early ages))
It's not completely manual. If you have cities A, B, and C and you have an existing route from city B to C, and you add one from A to C, it will automatically choose the optimal route by utilizing existing roads and connect the new city from there.
That's not what the original commenter is talking about.
The "decision" to build a road from A to C was not really a top-down decision from the medieval periods. Rome built roads in a top-down manner that sometimes benefited the Empire as a whole... but Feudal Lords built roads in a smaller and more selfish scale.
The growth of roads at that time was more akin to animal paths (animals deciding to travel the same path as other animals: because the well-trodden areas are flatter and easier to walk). Its an organic growth, rather than a top-down planned growth.
I seem to recall playing a few games where roads grew naturally like this, but I've forgotten their names by now. Feudal lords built Roads more akin to Death Stranding (where the player builds a road to try to connect to the online community. Once the road exists, you gain the benefits of the entire community's efforts)
So people are talking about that kind of "locally selfish but community building" behavior. And also in a management simulator and... not whatever Death Stranding is (First person Post-apocalyptic UPS simulator?)
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Different mechanics for different eras of history. Again: Civ6 probably is akin to some Emperor declaring a road should be built between two major cities. But Medieval / Feudal society didn't have top-down edicts from an emperor (at best: maybe from the Pope but... the Pope didn't have that much power). Having a simulator for the medieval time-period could be an interesting gameplay mechanic.
