I think i can help you with the “Lightmap UV are overlapping by x%.”. I had the same problem. As i am making a mobile game i overlapped my UVs
alot to keep texture sizes down. But then that messed up the lighmaps in maya. So i made a extra UV set in Maya, one that overlaps for texture. And one that does not for lightmapping. That got rid of the warning message and the weird looking light build.
As for the other problem, have you tried to delete history and freeze transformations on each object before combining?