There is a reason for the tight tolerance and lower clearance on the troller bracket to the casting decks on BCB models. We try to set the shaft angle so the propeller is pointing slightly into the water on an angle downward when under power. This means we have to adjust the mounting angle of the bracket to reach the right angle when deployed. Thus the stowed position is closer to the decks and tighter tolerances.
This makes the troller fish longer shafted. By reducing cavitation and gaining better thrust with improved propeller bite. It also makes steering considerably better as the trolling motor electric head is at a more level plane and consistent water pressure on the blades.
So you now know they are designed this way on purpose. Both MotorGuide and MinnKota are aware of the effort we go through to gain in this manner. We are not aware of another boats company that takes the usage and stowage angles into consideration with this much detail or consideration.