Clearly, the point was not about Canadian citizens and PRs but about those who are not.

The new system gives Canada (and, crucially, the U.S. authorities on whose behest this was introduced) an advance view of travellers about to board a flight for Canada, with a chance to deny boarding to people deemed undesirable. Beyond the "security" aspect of this process (for whatever it is worth), denying such people before they reach Canadian soil also conveniently means that Canadian authorities don't have to deal with asylum claims, deportations etc. at a Canadian airport.

The minor extra inconvenience to dual citizens and PRs from countries now subjected to eTA, who now have to travel with their Canadian documents, was an accepted side-effect.