It will keep the voltage constant but reduce the amount of amperage going to charge each battery. So if has an 80 amp alternator say the car needs 30 amps to keep the starting battery up to voltage. Say your pounding on the amp and its has a constant of 60 amps. Total draw = 90 amps. The battery powering the amp will eventually run out of reserve because you are drawing 10 amps more then what can be put back and the voltage will drop so low that the amp will no longer operate and no bass which is no fun, but youll still be able to start the car.

Now if the draw of the amp drops to say 10 amps, then there is plenty of amperage to go around and keep all the batteries charged. This is most likely the case because music is dynamic so the current draw will go up and down. The average is what is important not nessearily the peaks. With two batteries you probalby just have enough reserve so it doesnt have a chance to kill the battery before the draw lowers and it can recharge.

Say the amp draws 90 amps then the isolator will have to send all the amperage to the amp battery and have nothing left to send to the starting battery. Then the car will just keep drawing the 30 amps from the starting battery until no more left.

However its unlikely the amp will get anywhere near even 90 amps but if the fuse rating is 100 amps it is possible. It may not be likley but it doesnt mean it cant happen. You cant keep taking out more then what you put in and not expect to have problems eventually.