>Of course implementing this would require much AI scripting and perhaps some 'cheating' for the NPCs since they would get stuck. A larger graphical variety for Clonks would also be nice with this concept.

Well, two possibilities: 1) trying to create a working AI that does not get completely stuck (plus a bit of cheating) 2) very simple pathfinding AI on purpose
1: The player would rely on that the Clonks don't get stuck and rage if they do
2: The player would consider a working infrastructure (building ways between your buildings) a part of the settlement he has to care about. If his Clonks get stuck he would notice that his infrastructure is not as good as it could be and he has to think of a way to connect those two buildings where the Clonks get stuck inbetween. Of course we would have to provide the player with the means that are needed for such an infrastructure (ladders, bridges, hatches (to cover holes) and whatever more)

Further thinking: If we say that a working infrastructure that can be passed by stupid Clonks (think of the game Lemmings - they ARE going to jump off the next cliff), we can as well exchange the Clonks that do the production lines with something else so that at the first glance the player will understand why they get stuck everywhere ("WTF, how stupid is a Clonk????"). Replace the Clonks with Wipfs carrying some sort of bag or donkey-style animals - you could even extent it and say "Hey, if you are able to build a smart gadgetry to catch a bird, you can tame it and integrate it into your transport infrastructure as well."
That would provide the player with an ingame element that just went from "annoying" to "fun to care about and fitting into the Clonk style gameplay".