One problem is that the brood rearing is shutting down, so that the bees have lots more space in the broodnest, and (in my experience) the fall flow isn't all that strong, YMMV, also depends on the weather. By late summer/fall I usually have a partly empty deep on the bottom.
So they won't draw new comb and they end up putting quite a bit below where they do have drawn comb already.
I don't bother with the fall honey, since in my area it smells like gym sock tea. But if I wanted it, I'd imagine that I'd try to get the brood nest to the smallest size possible, no empty frames, and put the super on that. If they don't have space, then they will draw comb, as indicated. The stronger the flow, the more they will draw.