Hmmm. I'm going to put mine in MMB now and see what happens when I fly in a couple of months.

But he is a US citizen leaving the US after having entered on the US passport. I totally get why OP would want to have SFO-HKG on the US passport.

CX' system totally allows for different passports and visa to be attached to every single segment. OP had a muppet check-in agent. It happens.

I am often in the same situation with CX and it has never been a problem for me in BKK, HKG, CEB, MNL, SIN, EWR, JFK, LAX.

It really comes down to the individual checking you in at the time and how they were trained. I once had AA tell me I cannot transit ICN without a visa. On a solid passport. These things happen.

But its not systematic at CX to fail at this. OP's number was up and next flight will be fine again :)

OP only needs to present onward travel document to the check-in agent.

Do check-in agents ever ask for the document the passenger used to gain admission into their country? This is a serious question because I intend to do some entry fee avoidance by entering Chile on HKSAR and exiting Chile for Australia on my Australian passport next year (when entering Australia I am under Master Nationality Rule and cannot apply for ETA on my HKSAR).

They use Timatic or a similar system at check-in to see if someone is ineligible without a visa, passport less than 6 months, outward flight and similar rules because the airline is on the hook if you're denied at the destination for documentation errors.

It's an interesting question. Their rules say different nationalities pay something or nothing so it seems reasonable to arrive on the cheapest one. It's not a lie, it's more like nationality arbitrage.

Chile will probably want an entry stamp to match the exit stamp to mind you and they are pretty observant. Quiet but observant. For several reasons - dodging the fee of course - and to see if you entered illegally which is what they could think. Can you show them the AUS passport and also produce the HKSAR when you leave? Sure but then they know you dodged their fee so skip that.

All that said Chile immigration won't care if you can get to Australia or not as long as you leave so show the airline agent the AUS passport to validate you can board, put that in your pocket and show the Chilean immigration agent the passport you used to arrive. The four seconds they review your data is best the same data and while it is possible able to be cross checked with the airline, can't imagine it is or they have time to do all the cross checking. Worst case Chile asks for the dough which, IIRC you pay once for the life of the passport so it's not a continuous cost.

Missus and son have a British and Taiwan passport. Entering and leaving HK (and almost all other countries) is done using the British one. Entering and leaving Taiwan is done using the TW passport. So if travelling HK-TW, we'd show the British one during check in, then the TW on arrival, and vice versa. Haven't had a problem with this as long as only ever showing one passport.

We inadvertently showed both to CX checkin in HK once which confused the hell out of them. I simply took one back and told them to ignore it which eventually worked.

As a multiple passports holder, HK SAR being one of mine, you need to enter and exit a country on the same passport. This only applies to exit immigration.

The airline is shown the passport I will use to enter the country they are delivering me to.

I show CX check in both my local immigration exit passport and destination immigration passport if they are not the same.

Airline and immigration are two different things. Airlinesjust want to make sure you have travel documentation in order. If you use a different passport at immigration is really not an issue.

Should you?
We've been saying this confuses check-in agents above.

To clarify:

When two passports are shown I specify this is my exit immigration passport and this is my destination immigration entry passport.

And it doesn't confuse check-in agents?

OK...but I plan to withhold my entry passport to check-in until asked (just present next destination passport). Similarly withhold next destination passport to immigration (just present entry passport).

I'm pretty sure immigration won't ask for my next destination passport.
I've never encountered any airport check-in who's asked for my entry passport though...have you?

I have been ask for proof of entry to the country I am departing from which is not in the same passport I use to enter the destination.
Maybe not by CX check-in, but definitely in SE Asia and Central/South America.

as you said, "if don't ask, don't tell" is very often the best way.....

Immigration officer don't care where you go once you leave....

In some countries in Asia, Check-in agent do check your entry stamp.

I have been ask for proof of entry to the country I am departing from which is not in the same passport I use to enter the destination at check in.
Maybe not by CX check-in, but definitely in SE Asia and Central/South America.

I recall both MH and CX do that to me at BKK a few times now. I find it irritating. Like.. Why do you care when and how I entered here. You are only liable if you let me board a flight to a destination or transit where I do not have the correct papers.

Maybe Prayuth is building some sort of Stasi to help check on foreigners. I also saw AVIS Car rental at Silom and Hertz at HKT want to see entry stamp in passport!

Just my 2 cents but there are lots of foreigner overstaying their visa in Thailand, so that's probably the reason....