4QJosh-a places the altar-building episode at a different point in the narrative than the Masoretic Text. Isn’t that a structural difference, not a copying slip?

Correct, and this is a case where Qumran may preserve an older arrangement, since Josephus also seems to know the altar episode in that position. With only two copies the base is thin, and Joshua is one of the books where the text form genuinely varied in this period. It does not undermine the claim that the book’s content was preserved: the same events appear in both, in a different order at one point, and the difference is on the table for anyone to weigh.