Good point. Especially worthy of consideration given the nature of the polarity reversing switch on the box–middle position is off, and the two outer positions reverse the polarity, with no indication of which is which.
One could mark the correct position, but in practice that is insufficient for an application that might be damaged if connected backwards. One very frequently pushes the switch too far in the attempt to turn the box off, switching the polarity before power is finally cut.
The switch does have an axel hole built into it, so one could make a custom cable with one end suited to the BrickPI, and the other (battery box) end either limiting the switch’s movement between off and one of its on positions, or alternatively holding it in one of the on positions (both options allowing the cable to guarantee correct polarity).
Be aware, though, there is a small LED on the battery box that indicates the box is live. It doesn’t burn much, but it shouldn’t be left on permanently.
Best option (I think) is a custom cable that limits the switch between off and one of its two on positions, guaranteeing correct polarity.
Second best option is a custom cable that holds the switch in one of the two on positions, and has to be uncoupled from the box to turn the box off. Given that the electrical connection to the box is a single-position studded lego connector, the second option isn’t less functional by any significant degree. It is foolproof, and simple. It would just a little less elegant. You might even call it klugetastic!