The soul, on the other hand, does not have a physical component that we've found, so removing it would not necessarily result in any physical change (excepting the death of the target). Thus, the difference between the physical and the metaphysical object is relevant.

I think the reason you were downvoted is the fact that a very large proportion of people on this blog (including Eliezer) believe that if their is a separate component we could refer to as a soul (or consciousness, or any similar concept), that it is entirely contained within the real world - that is, it is going to be some component of the brain instead of any sort of separate metaphysical property.

I don't think it's fair to downvote you for that, since the opposite is clearly the prevailing opinion in the HP universe.

However, given Eliezers extensive arguments against any sort of epiphenomena, I think it is highly probable that it was the mention of the soul that should have set off alarm bells for Harry, because SuperRational Harry shouldn't believe in a soul, at least not without major caveats.

I think the soul question is going to come up in the eventual direct conflict with Voldemort, and that it is going to be a Very Big Deal. It is the source of Voldemort's immortality, after all. It's the most important question Harry needs to answer, and he hasn't even asked it yet.