When cranking the starter, the battery voltage is lower because of the current drain. Most all older ignition systems were designed around this lower voltage (sometimes much lower than typical cranking voltage to ensure that the worst case conditions like low batteries or very cold are considered) so the use a "ballast resistor" to reduce the normal running voltage to the lower design voltage. But during starting, the full battery voltage is used (as full as it can be) to ensure a good spark for starting. I am assuming that the second click out position on the switch is full battery voltage, and one click in is the reduced running voltage. With a stock Pinz wiring, this switching is done through the starter button (reduced voltage normally but full battery voltage when the starter button is depressed).now i need to make sure these electronics are not getting the full 24+ volts!
However, whoever made this modification may have added the separate ignition switch because they used a 12V ignition system. Is there a wire that connects between the two batteries (where the + of one is connected to the - of the other; there should be no wires other than between the two batteries. If there is any more wires then they probably are using the "lower" battery for a 12V source. This is bad practice, and usually means the batteries will need replacing much more often). Let us know if there is this additional wire between the batteries.