I have a fair number of headscratchers about this game..

[Hunter of Shadows]

What Hunter said, Alexander most likely concealed them under clothes so as not to frighten Danie along with making them carry around clove and sage too (to cover the smell of walking corpses and what not. Would explain why they avoided him.

I've smelt enough roadkill to know that clove and sage wouldn't mask the scent of rotting flesh. Even when burnt as incense they don't have a strong enough scent to mask that very distinctive odor.
It would be more likely that Alexander had some sort of alchemical Febreeze like substance.

The gatherers aren't necessarily rotting, you gotta remember, the gatherer's were formed from still living people, who drank some spiked wine with the summoning potion, the entities that have done this to the humans, may be capable of keeping the body ALIVE, even in the horribly twisted state we see, what does this mean to your question?

Simple, the body is still rotting from the many open wounds you see, but not nearly as quickly as it would be if the body was dead

As for the key, Daniel likely took Alexander's advice to heart "You can never be too careful" and made a copy of the key, and hid it, because as you all pointed out, it's unlikely for Daniel to have hidden a key himself, that would only make life more difficult, he likely thought that at some point Alexander would realize that Daniel had developed a conscience, and got rid of the original key himself to hinder Daniel's progress.

All pure hypothesis