Rocket7First, note that "had" precedes a noun, so it isn't being used to form past perfect. It's simply serving as the past tense of "have."
A: Your analysis makes sense. The initial modifier (before the comma) serves as an adverbial modifier showing how anthropologists support their argument. Then we have the main clause ("anthropologists argue") followed by a dependent clause showing the substance of the argument ("that these ancestors had hearing . . . ").
B: "So" introduces a consequence. So . . . the meaning here translates to "Using enhancements, anthropologists argue (about what, we have no idea). Therefore, these human ancestors had hearing similar to ours." This makes no sense! We don't have to worry about the antecedent for "these," since it is followed by a noun that specifies what we're talking about.
C: Placing "anthropologists argue" between commas makes it NOT part of the main action, almost as we had "she said" in that spot. So C translates to this: "Anthropologists argue that human ancestors used digital enhancements to have hearing similar to ours." That's clearly not good! It's not just awkward. (In fact, "awkward" is very really a good reason to cut out an answer choice, except when we are relying on intuition.)
D and E: These both place the human ancestors in the subject position. That would make the initial modifier apply to their action. Since our ancestors weren't the ones using digital enhancements, we can cross these out immediately.