Devils Advocate, China is one of the (few) countries that takes all of the crew's passports on arrival, and returns them with an entry and exit stamp for TRANSIT flights - absolutely ridiculous!!
I guess it's to check that each crew member has a current China visa - the cost of which is a couple of hundred USD's per 6 months - simply to transit or turnaround, and NOT leave the airport precincts. As such (because of the cost), not all pilots are issued visas, which in itself is a blessing for those who aren't, because - as you can imagine - the visas take up a full page, and the entry/exit chops amass fairly quickly.
One can only GUESS what the penalty would have been, had he (the JAL Capt) arrived, minus his passport - probably an impounding of the aeroplane.