That's how the system works. But for the HV battery to charge the 12V the 12V needs enough of a charge to connect the HV battery. And the HV battery cannot be at a low state of charge. The 12V is the sacrificial lamb in that case.Assuming the system is monitoring the charge on the 12v battery, it seems a simple solution would be to have the HV battery come back on to top off the 12v when it drops below a certain level, just as a backup, then shut back off. First priority would be to find the vampire sucking the 12v dry though.
When your vehicle is off the 12V is running the show waking up systems as needed.