Patrick, please read my whole comment under MDL-12221.
One aspect about backwards compatible themes:
1.9 themes can't ever be really compatible to 1.8 because several CLASS names have changed from 1.8 to 1.9.
+1 to implement the enhancement (compatibility arguments not really count).
Different themes for 1.8 and 1.9 are necessary to follow these differences. In these different versions you may also implement the small header changes for 1.9.
@Martin
The need for consistent container handling has been brought to recognition with the work on the custom_corners theme. Inconsistency and hacks have not been an issue for many developers until now. I have already been struggling with several Moodle pages due to this inconsistency in the past. I am glad that Petr is working on a solution.