I kind of have issue with this, as well. If you're truly going for the theory that Remus can smell an Animagus, that implies that they have their own distinct smell away from human or any other animal form. You've singled them out, you see. So, I think that Peter could smell like a rat to other humans, but to a werewolf there would be just a slight difference or an extra fine underlying layer not perceptible to humans.Good point. That is also in the story. He was a human, giving him his distinct smell, but he was a rat and the rat smell probably covered most of his human smell.
Crookshanks is not human and Sirius admitted that the cat knew straight away that 'Padfoot' wasn't what he appeared to be. The same with Peter, which is why Crookshanks was attacking him all the time.
I think you could say that he smelled like a rat, but detail the special something that only Remus can smell.
As for Remus' scent, do you want all werewolves to have a particular smell, or each one differently? Please be careful with the chocolate thing. As one of the many Remus lovers, I can tell you that it gets a bit trying. If your story is more light and humour, then I'd say it could work, but other than that....
Yes, Remus gave out chocolate uring PoA, but no one seems to pick up the fact that he was the DADA professor, so he was well versed in the Dark Arts. He also knew, as I'm sure all of the staff did, that Hogwarts was going to be surrounded by the guards of Azkaban - Dementors. The effects of chocolate clearly combat the effects of the Dementors and that is why he carried it around, not necessarily to feed some chocoholic need. He was brilliant, after all , and even Madame Pomfrey compilented him on finally being a DADA professor who knew what he was doing!
~Michelle (The One Who Marauds... with Remus, always)