I'll postulate a theory here.
when you have voltage in parallel, current varies. ( ohms law )
now at the beginning of your charging process you have one battery charged or nearly charged, and the other nearly drained.
What will happen is the sensing circuitry in the regulator will determine that not much output is needed because of the higher charged battery and will slow the charge rate considerably. You see this when you jump start a car and only get a "surface" charge.
Now IF you provide to the regulator a voltage sense based on the current status of the lowest charged battery ( which is essentially what an isolater does ) then the isolater will channel the current to the battery that needs it the most and feed some bias back to the more charged battery to test it to see if it now needs charging.
Hope that helps some