Earlier quoted context omitted.
They're closer together, but the distance traveled in total is the same. Imagine the transistors are pieces of paper, and you're drawing a line over them. If the paper is flat, then you're drawing a line of distance n , and the points are n apart. If you fold the ends of the paper together, then the points are 0 units apart (or near enough to make no matter), but that line still has a distance of n .
The previous commenter wasn't talking about this transistor 3d feature, but about stacked transistors. Just like a city full or high-rise buildings can pack a lot more people in per square mile, a stacked transistor IC could pack a lot more transistors per square mm.
We need pin outs and thermal conductivity - stacking layers of transistors is bad for both.