I found, in practice, that the divide and conquer approach led to weird altitude artifacts, where different divisions would result in different heights, so the point clouds didn't line up. Could have been a one off bug though.
Amazing piece of software! I've a question. It's a bit unclear to me, is there a global adjustment applied to the sub-blocks that would help with the overlap issues?
There is; the alignment uses affine transformations, but it cannot account for certain cases (e.g. severe bowling effects). It's an interesting area of research.