Does each motor use a different starting battery? I think they would have to.
Assuming the batteries are in good shape AND charged, I would expect similar charging voltages ( idle speed voltages might be different a bit)
Are the voltages different by the same amount after the motors warm up?
Either way, unless one motor's battery has much heavier load on it, the voltages should be close.
Do you have a shore powered charger running and if so, when you first get on the boat after sitting for a whilw ( day oy a few days) what does the charger indicate.
If for what ever reason the bilge pump is cycling or worse and you do not have a charger connected and operating, the batter that the bilge pump runs off of may be getting run down.
Worst case, there is a problem with the engine that only makes 13 volts.