In regards to your second-last paragraph, what has changed is that you are no longer hunting.
The exemption in the transport regulations explicitly applies when transporting between hunting sites. Travelling home at night would not seem to fit that description, so it would seem the exemption does not apply, and the muzzleloader should be unloaded.
Likely it would have to be unloaded for overnight storage at home anyway, unless you are headed to a hunt camp in the 'wilderness', or you live in a location where you are already legally allowed to have a loaded firearm for pest/animal control temporarily stored in your house.
I think, like the target shooting from the boat issue, that it would be up to the CO/OPP/RCMP officer's discretion at the time, and, like you said, maybe the courts for a true answer.
That's how I read it anyways.