Good points.
What about picking up a BW permit and an MN fishing license as well? What's that like an extra like, what $50 bucks tops? I don't think you need to register out of state canoes when you bring your own into MN these days. (No real clue there though.)   Might consider an RABC to go back and forth? Yeeesh, seems like too darn many rules when you play the border and switch sides a lot eh?  ;D

A few portages really don't sound all that bad compared to anticipating all the possible legal scenarios not to mention wind issues.