Actually, perhaps my experiences have been clouded by my travel pattern. Most of my recent holidays have been in Japan, so all the check-in experiences were specific to Japan => Hong Kong.

Come to think of it, the two times I flew outside of Japan, there were no questions regarding my HK status, and in fact I was allowed to use my e-boarding passes by just showing the passport (which contains no HK endorsements inside). When flying from Japan, I was never issued with an e-boarding pass, as the website stated that a document check is mandatory.

The two places I flew from outside of Japan were Taiwan and Singapore.