FOLLOWUP: Another thing that might be expected of a UV generator is a consistent winding orientation of UVs. (Left-handed, since this Unreal.)
It turns out that while the output of PatchBuilder and ExpMap is mostly left handed, it is NOT always left handed. For me, this resulted in have triangles that appeared to contain no pixels, since I was relying on winding number to check whether a pixel was inside of a padded triangle.
This became much more apparent when I switched to using XAtlas, which seems to orient triangles randomly.
So, once again - it might be expected behavior or it might be a bug. But now you know to expect it!