How clean is clean? Does your first shot out of the case match your last one shot while sighting in? Just like in baseball, if it works then stick with it. Shooting with a shiny clean barrel didn't work for me in the past. The first shot always ended up as a flyer. If I was shooting my rifle, then I would agree with you. A muzzle loader requires enough wiggle room to make loading possible. The wiggle room allows pressure to escape around the bullet. The fouling acts as a gasket to make the pressure more consistent. If the conditions are the same, then I can repeat the results.
As for the rusting and pitting after 3 days. I'm not sure what to do about that. Muzzleloaders are a little more high maintenance, but you raise a good point.
From those who much is given, much is expected