you move a window part lower than the bottom of the window, a position which has no meaning.

1. Correct, but what if it is a pocket window?
2. If you use a roof part with a window already inserted (from a wall) will be also no problem.
3. If you make a hole in the roof and insert manually a closed turn window (like in this post )
you will have problems with the elevation every time you open the window.
Anyway in the future release of RG-4.5 the holes and windows are automatically created and inserted on the roof in the correct position
but I can't avoid future window elevation modifications.
My workaround was to mentioned this in the future user manual of RG.
Probably I will need to elaborate a little the operation for users:
new elevation = old elevation - (new High - old High)/2
or something similarly with more screenshots.
As you can see there it is solutions for everything [:)]