Yeah. That's why it works about half of the time. In the cases above, it simply won't work.
In Battle of Olympus and Faxanadu, it happens in one screen rooms.
In Adventures of Lolo, you only have 1 screen per level.
In Godzilla, the top and bottom 3rds of the mountains are in the foreground, but the background is an entire strip and contains the middle of the foreground mountains. In the stage select screens in the 2nd photo, it is only a single screen.
Your explanation makes sense as to how I was able to get it to work in a lot of instances, but until there is a feature made that allows some sort of manual splitting of pre-determined sprites, there are going to be a lot of games that just won't work.