At the moment the fact is that despite the old FITS usage and the recommendation in the WCS document many file from camera are top-down.
This the case at least for the two I can test, indi_gphoto that return the FITS rows in the same order than libraw and for indi_atik from the Atik SDK. This is probably also the case when using other manufacturer SDK.
But it is not necessary to change the way the data are written to the file because this can affect the performance. So probably no alignment code need to be changed.
The idea with adding this new ROWORDER keyword is to clarify the way the processing software treat the image specifically with bayer matrix. All of this with minimal change in the capture software.
So if a driver know the camera return data in top down order it just add ROWORDER = 'TOP-DOWN' in the header, ROWORDER = 'BOTTOM-UP' in the other case.