For a visa-exempt traveler, it should be fine. When boarding the plane in Cuba, you can travel on visa-exempt passport as a visitor/tourist. And when you arrive in Canada, just showing the COPR/passport is good enough and the Canadian officer can see PR status on the computer.
My wife did exactly this when we traveled to Mexico a few weeks after she landed.
Of course if you are not visa-exempt and your passport requires a special visa to visit Canada, then you need to arrange for a travel document as you would be denied boarding in Cuba without one.
The travel document is not for the Canadian immigration side, it is for when you are trying to board the plane to return to Canada. The airline staff do not recognize COPR as a valid travel document, so if you don't have a visa-exempt passport and don't have PR card... the only other option is to show them a travel document.
Once in Canada, ANY port of entry will be able to determine your wife's PR status from just her COPR + passport. Your only concern is boarding the plane in Cuba on her visa-exempt passport, which should not be a problem.