With the eTA leniency period about to end, I'd love to know how the airlines will process check-ins after September 29th.

For eTA holders I assume that the application is tied to their passport number. So when the agent/kiosk does a swipe a go/no go flag is given perhaps?

Canadian and US passport holders are exempt but how are airlines going to deal with Permanent Residents? There is no definitive link between a Permanent Residents passport and their PR card. A Permanent Residents passport could change during their PR card validity period voiding any semblance of a link that would have been established when applying for the PR card.

Are airlines going to physically inspect PR cards on check-in? Will they swipe them? I know PR cards are machine readable but are completely different to passports. Surely airlines haven't invested in new PR card swiping tech? Will agents have to manually enter PR card details?