Maybe it's just my perspective, but I think people are pushing the Dante's Inferno angle way too hard. To me, they are using the idea of descending presented in Inferno, but to illustrate the 7 stages of alchemy (which makes sense, given the context). To this I add that many historians now believe that the search for the Philosopher's Stone has always been a metaphor for developing one's own spiritual awareness/psychological understanding, and that the stages in alchemy were intended to transform the chemist as much as the chemicals he worked with. Let's say there's a reason it's called the Philosopher's Stone and not the Ruby of Immortality.
If I'm correct, most of what you see is meant to be representational.
The pointy black hoods of the figures may refer to crows, which were indicative in alchemy of the process of calcination - the burning/breaking down of matter to it's basest parts. Once broken down, the matter was considered purified and ready for further development.
In short, I think these guys were meant to break down the cast (psychologically). They always just threatened, never caused real damage. Plus, when we meet them, they are in a room with chalky-white reliefs on the wall (which come to life); possibly people who went through the process unsuccessfully. Chalky powder is a common residue left behind from calcination. Lastly, they have white faces under their black hoods and symbolically speaking, the crow - after calcination is complete - pulls back it's black feathers to reveal a white bird.
It's just a theory and there's certainly parts of the movie I cannot explain.
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