These are totally understandable questions that you pose in your emails. I'll try to answer and explain below.
First, your map will work correctly in Custom Maps. Custom Maps always displays the map image in its "native" orientation, as rotated bitmaps become relatively blurry on lower resolution screens. I guess very high resolution maps (>16mpix) on very high resolution screens (>300 dpi) the rotated bitmap images might be legible, but by keeping the actual image orientation maintains the best map image quality regardless. In the early days of the app I played around with rotating the map images to north up always, but I decided it wasn't worth it with the degraded image quality.
Second, the orientation is saved in a matrix that converts your geo location to map image coordinates and vice versa. It is just that Custom Maps always display images without rotation.
Third, the kmz file should display correctly oriented when opened in Google Earth (at least on desktop). Google's support for image overlays on the web map products varies, and many of the newer versions may not support all features of image overlays. If you use only two tiepoints, the resulting kmz file should contain the simplest possible markup for a rotated image overlay, but it is possible that the image overlays are not always properly rotated when displayed in Google's web pages. If you use more than two tiepoints, then the resulting markup is more complicated (but still valid kml) and the image overlay is even less likely to dislay correctly in other tools that do not support all aspects of kml image overlays.
The best way to get "independent" validation of kmz file created in Custom Maps is to open it in the desktop version of Google Earth. My understanding is that Google Earth has the most complete kmz/kml parser of Google products.
I hope this helps. Feel free to ask more questions if I missed answering something or if my explanation was not clear.