What other distinction is there besides the soul being fictional/supernatural?
That
is the distinction. The soul is dualistic, the mind is not. The mind is just the software running on some sort of strata, the soul is some other spiritual concept somehow associated with consciousness. It's not a question of discovering it or not, because if the soul exists, it exists in a manner such that it doesn't need to be discoverable.
The transporter moves not just physical matter but everything, including the thing we currently call dark matter.
Based on
what? Dark matter doesn't interact with baryonic matter by definition, it's not like it's necessary for life processes or anything. It's not even detectable except gravitationally. And I am saying that
even if it did transport only baryonic matter, it wouldn't somehow abandon the soul, because the soul is by definition something immaterial and Other, and it isn't somehow physically associated with the body.
I mean, you're arguing against a conclusion I'm
not making. You're arguing as though I'm saying the transporter
would disconnect body from soul. If you're going to argue with me, then argue against
what I'm actually saying: that the transporter doesn't
need to move the soul, because if the soul exists, it exists in a manner such that it doesn't need to physically travel with the material body. I'm not doing this ridiculous "god in the gaps", "MAYBE SCIENCE CAN PROVE RELIGION SOMEDAY" thing.
Edit: You know what this is? It's another definition clash, because of not defining terms.
When you say soul, you seem to mean "some not yet discovered phenomenon that happens to coincide with many of the properties ascribed to souls by various religious beliefs".
When I say soul, I mean "a spirit or ephemera beyond the constraints of the physical universe that is the essence of being". I'm referring to the actual theological concept itself. I'm saying that if some religion in reality happens to be 100% right about the nature of the soul, in both observed properties and spiritual aspects, then there is still no a priori reason why a transporter would separate such a thing from the body, any more than (to use your example) a reason why walking around would do so.