I will probably be tarred and feathered for this but.... I have never been a fan of 'Insertion' of any objects, with the exception of Doors and Windows. As you mention, initially every inserted object just sort of goes where it wants to, which forces the user is reposition, flip, etc. The advantage of cutting a hole in a roof is that I can have control over the exact location of the skylight in relation to roof framing members and placement at room centers or over other chosen object (eg: kitchen island). Not only does this give me accurate section views but also the ability to precisely dimension and callout the location so that framers/builders have total clarity as to my intent. Old school, but effective.