Why don't they use more than 12v in high power car audio?
Bass drops and batteries.

There is only one way to handle an instantaneous power spike that exceeds the capacity of the alternator, and that is to draw it from the battery.

If you were to rebuild your secondary alternator to produce 100 volts (completely possible), and then purchase and install gear that used that for power, if you do not subsequently attach a battery bank that is rated for that same voltage (or boosted to pretend to have that voltage), then you only have the output from that one alternator. Period. Exceeding its capacity will break it.

In the current method, you have access to the output of both alternators and the battery that already had to be there for the car to start, and you didn't have to buy a second battery or the booster to make it play nice with a 100 volt system. Doing what you propose halves your available power and requires at least one additional battery or battery bank.