When you say, "I didn't want to accidentally reverse polarity, and burn up the board", I assume you are talking about Sergey's board. Sergey's circuit board is protected against accidental reversal of polarity. And, if you connect the MC the way I told you, even if you reversed the motor, it will ONLY affect the motor, not the whole of Sergey's circuit board.
Also, I agree with you about only needing the forward control. The switch is unnecessary. I never use the reverse function.
You said: " I can also drop the fully charged voltage of the cells with the MC below the capacitors limit this way."
Yes, but you are also limiting voltage to the whole of Sergey's board the way you have that configured. What is the point of using five or six batteries if you limit the voltage to the Sergey board? You need that voltage as high as possible for the solenoid, right?
I really suggest you wire it the way I told you to.
Anyway, do what you want, it's fun to experiment.