I've done some digging. This is pieced together from scraps of info and old patent documents from Boeing, a couple of incident reports and googling so is definitely subject to correction. Perhaps an engineer can step in with a better informed post!
The two smells seem to be the chemical additives used to help us pilots detect a leak:
Orange peel = D-Limonene
Pine Needles = Methyl salicylate
Connecting the dots it would seem that the toxic rain repellent (do we still use Rainboe??) uses D-limonene, and some of the more recently developed non toxic repellents use methyl salicylate.
Therefore when the manuals differentiate between the toxic vs non-toxic smell, I believe they're saying it depends on which aircraft, therefore you'll have one OR the other.