yes that is correct - you can actually run BPP twice if you want, just making sure to specify the same image as the reference image both times. i havent used BPP in a while but i think it would not matter that the reference image is not actually in the list of Ha files.
in fact you probably have to do it this way, because you need different flats for the Ha-filtered images. i dont think the script necessarily knows how to handle OSC images which are filtered.
rob