I had my COPR expiring in a couple of weeks and had a confirmed ticket. I called Air Canada a day before my flight and they said the same 'things changing rapidly' and asked to try and check at the airport'. So I took a chance and was ready for both outcomes.. allowed to board or disallowed.... I followed airlines guidance and instructions and did whatever I could within my rights. Even the CBSA officers were very helpful and greeted us into the country well. So I don't see it like working against instructions.
In terms of the Self Isolation rule, they are recommending everyone to self isolate for 14 days. Its not quarantine... you can still go out for grocery and necessities... but no unnecessary interaction with people.
I have a place to stay here for a few days and didnt need to worry about food and grocery.. so worked out for me. Everyone's case is different so you do what suits you best.