Questions : Regardless of how my batteries are combined the alternator will at some point be charging 1 almost full battery and 1 almost empty battery bank, so what charge level (voltage?) does it use to determine its output ?
If there is one voltage regulator for both batteries the charging device will see a voltage that is a combination of the two battery voltages. If both batteries were the same size, the voltage would be close to the average of the two batteries, but if one is a lot larger than the other, then its voltage will overwhelm the other to some degree. A large house batt at 11 volts and a small starting batt at 12.6 volts might result in a combined voltage of (guessing) 11.5 volts. This means the charger will pump out close to its maximum......but most of the current will flow into the house batt that needs it.
Bottom line.....don't worry about it, except in the case where you do not charge for very long and the starting battery has the potential to give up some of its charge to the house bank.