I believe the factory wiring was done to provide maximum power to the lower right flipper (for the power stroke). The thought was the flipper needs maximum power to get the ball up the ramp to the upper playfield. Once the power stroke has completed (the EOS opens and the stacked switch closes) power can be provided to the upper right flipper.
I have done this modification to my BK2K and have noticed no problem with the lower right flipper making it to the upper playfield. I like the double leaf switches for flipper control.