Interesting. I am dual citizen Canadian/Euro. I use my Canadian passport for all of my flight bookings. When boarding I show whatever passport comes out as ID - since it really doesn't matter. When I land in whatever country - Asia, Europe, Australia, SA - wherever - I show whichever passport is the most convenient - regardless of using my Canadian passport to purchase the ticket. Of course the USA is different - that's what Nexus is for.

For Australia I usually get my visa assigned to my Canadian passport and use that to enter but the odd time I have registered the visa to my other passport - just have to ensure you enter the country with whichever passport has the visa.