Thanks guys for the reply.

Now I am glad that I started this thread so this can become a future reference for someone else in a similar situations. I am sure that there are more than a few Canada PRs travelling by air without eTAs. I will go to the airport earlier tomorrow and also report back what happens tomorrow.

I am prepared to show the check-in agents the CIC (Immigration and Citizenship Canada) official information. Hopefully they will believe it (it clearly says "You do not need an eTA if you are a permanent resident of Canada." and "Canadian permanent residents cannot apply for an eTA.") and there will be no system limitations on their computer blocking the check-in unless there is an eTA.

I will be originating from HKG checking in at the J line. Hopefully being the home port of CX, they will have proper staff to handle this and if needed there would be managers from the J line who can help with the situation.