But does the smell itself cause suffering regardless of whether it can be percived as good or not?
No, in most cases there would be no “objective” reason why a smell would necessarily cause pain. I image in a few cases, there could be such a reason, just as we see objective causes for pain in the sense of touch (e.g. when someone gets burned). However, this kind of sensual pain was not possible in any of the senses for preternatural man.
There clearly was a radical shift that occured in the natural world when the fall occured. For instance, how would it be possible not to have rapid change in climate, or that men wouldn’t have to till the ground and pull weeds. I think the answer is that there are other possible conditions for matter, which lacking direct experience with, we find difficult to understand–even paradoxical at times.
Matter, as far as we know, is not capable of passing through other matter (seemingly occupying the same space at the same time) yet, we have eye-witness accounts that this is what happened after Christ’s Ressurection–he passed through locked doors. Matter must be capable of existing in a glorified (or preternatural to bring it back to the point at hand) condition in which it possesses accidental properties unfamiliar to us. It remains, however, the same matter. Thus, Adam and Eve didn’t have different bodies after the fall, but their bodies had a different condition–a fallen state.
As might be obvious, all men suffer the same lack of knowledge, so that while you or I might be able to posit how such things are possible, without direct experience, it is almost impossible to truly understand.