I had two itineraries last year that may help to explain:
* I went to PVG for a lunch meeting and then back to HKG. When I checked in at HKG, I asked the KA agent to not issue me the return BP. She said she could not do it for PVG anyway.
* The other is my PEK-HKG-PVG flight. I could not check in at PEK all the way through to PVG. I have to check in the second segment in HKG.

My feeling is that from flights originating from HKG, roundtrip transits in China are not allowed, and for flights from a port in China, transits via HKG to the same or other ports in China are not allowed. They are not taken as transits.

Transit via NRT (on JL) is an option: HKG-PEK-NRT-TPE.