Yeah, I'm pretty certain Air Canada will not ask you about proof of residence if you're leaving Canada. That's not the job of the airlines and their only job is to make sure you have a visa, PR card, citizenship, whatever allows you into your destination country. The only time AC is going to ask about documents allowing you into Canada is when you're checking into a flight headed to Canada. And even if some weird anomaly like emma69's case happens, Malaysia isn't a country that demands API as far as the lists I've seen.

What I know is that only certain countries demand API and Malaysia isn't one of them. Malaysian authorities likely will not demand anything aside from seeing your Malaysian passport. If you book separate tickets and tell them you were in a third country this whole time, it stands to complicate things further.

A lot of this has to do with knowing people who have done similar extensive travel. Many of my friends are Saudi-Americans, and they book flights from the US to Saudi via a European airline and they use their Saudi passport info (mind you Saudi isn't a country that demands API edit: it's possible that Saudi demands API). Despite the API, U.S. authorities never asked them about their Saudi passports presumably on the API system whenever they landed in the States. They just show the proper passports at the proper times and they've been doing this for 20+ years. I imagine it's similar in Malaysia.

Either that, or if you want to play it extra safe, fly into Singapore and enter Singapore using your Malaysian passport then get into Malaysia by land.

It might not make much of a difference if you book your ticket on either passport as long as you know which passports to present, but if you want to play it safe with Malaysian authorities, book it using your Malaysian passport.

Bottomline is: it's not that complicated so I don't advise you to complicate things with separate flights and separate legs of flights, and it'll go well.