Hermione is well aware that Muggles isn't exactly the most scientific word, but then, the wizarding community doesn't really have much in the way of scientists. So she wouldn't have been insulted if Mac had chosen to comment further on it, given that it was a silly enough term even within a vocabulary that included words such as Floo powder and flobberworms.

She nods at the mention of witch burnings and inquisitions. Those had been an unfortunate part of her own world's history as well, and a major reason behind why the magical world had largely retreated from the Muggle one and instituted the International Statute of Secrecy, among other things. Though something in what he says strikes her, she lets him talk, trying to piece everything together and not wanting to interrupt.

It soon becomes clear, though, that encompassing such a large portion of history into a short, simple summary is nothing short of impossible, so she decides that asking a few questions should at least help him shape his tale in such a way that she can actually follow it.

"So this Traveler is the embodiment of good, whereas the Darkness is that of evil? That sounds a bit too black and white, doesn't it? Even where I'm from, the Dark Arts aren't so much evil as they're used to harm people, which means that sometimes - though rarely - they can be used towards good people towards the right reasons."

She pauses, then, before lowering her voice and trying not to be insulting as she asks, "And-... I'm sorry, but you keep saying 'we' when you talk about humans. Does that mean-...? It's just, well, you look like a Qunari, so unless you normally look more human-like or they've evolved to look quite different from what I'm used to...."

In case the round of questions don't make it clear, yes, Hermione clearly wants to know whatever Mac is willing to tell her.