OK, I understand your question/concern and it has nothing to do with the alternator, simply the way the isolator is wired.
That jumper means that the alternator directly charges the jumped connection. There is no diode protection against discharging. That is a little weired but maybe not fatal if that battery is not critical to engine starting. What is that other battery used for?
But it really doesn't matter except for better understanding. It could be a house battery or a bow thruster battery in which case it would not likely be discharged from the other starting battery running down.
I would just wire your new isolator without the jumper and it will be just like the Mainship I described above.
Now if you want to discuss the pros and mostly cons of isolators.....;-).
David
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