Australia to Shanghai overnight flights are indirect via HK layover.

The overnight flights from Sydney to Shanghai Pudong have a 2hr stopover in HK. So my itinerary would look like this:

Sydney > HK > Shanghai (Jiangsu province factory visit 2 days) > HK (2 days) > [Tokyo (2 days) ]> Sydney.
[Still confirming the Tokyo visit].

Am I allowed the 144hr free transit with the overnight indirect flights?
AND would this itinerary work or would they see it as going in/out of HK? I may be able to re-arrange Tokyo/HK order.
What if the Tokyo visit gets canned, would it still work?