She can land in Quebec but she must have proof of onward travel out of Quebec else is likely her landing will be refused.
Whilst in theory she could arrive as a transit passenger, complete her PR landing showing her onward travel out of Quebec, collect her luggage for customs inspection and just abandon the onward travel sector by leaving the airport that is something you will need to decide if any issue in doing that.
To avoid issues maybe the best option is to fly to Toronto complete a landing there then connect for a domestic flight to Montreal allowing 3 hours for the connect.. CBSA at Toronto will have no interest in any onward flights that your wife has and she does not need to tell them but ultimately decision is yours and your wifes on which option she feels more comfortable with.
Cost wise you are still faced with a connection ticket which ever way around you decide.
Just to add that taking the Quebec option probably not a good idea to give a Quebec address to CBSA for the PR card and leave applying to post landing.