I haven't read that book or heard of Pai specifically, but that definitely matches what I have heard from my friends who do Asian archaeology and from the professor whose premodern Korean history class I audited. When lecturing on the ancient kingdoms of Korea it's hard not to talk about the allegations that the Japanese occupation forces destroyed evidence relating to the same. And in general, her argument sounds like it makes a lot of sense, just from how these things tend to go.

Re: Ch. 11, yes, I think so, with the twist that it was not a positioning that the Koreans themselves were content to accept--apparently the standard pejorative term for Japanese people pre-annexation was "dwarf barbarians."

As for the elites, it's not that I doubt Duus' version of the facts, except for the parts where he admits that there's just no way to know exactly what happened, such as what really went down when the protectorate treaty was signed. But more discussion of Korean society and politics in the late 19thC pre-opening might have been nice, to try to put all of this in context. My premodern class stopped around 1800.