First off the HVB will never be fully drained enough to be an issue. Once the plug-in charge is depleted the car drops to a hybrid mode where a small portion of the battery remains maintained by the engine as needed. You'll easily notice this when the battery gauge on the dash changes to the '2D' one without the miles listed. It'll regularly cycle up and down as you drive. Same as any other hybrid vehicle on the road. When the car is sitting and off, the HVB is completely disconnected from the rest of the car so there should be virtually zero drain there. On top of that, even at the lowest it will let you drain the HVB, there is enough actual capacity left in it to start the engine and not leave you completely stranded. In fact I don't think I've read of anyone so far being unlucky enough to have it drained far enough to be an issue.
As you read, the car does use a DC-DC converter in place of an alternator to convert juice from the HVB to the 12V battery. This is only active while the car is in 'ready to drive mode' or in some cases while plugged in and charging. If out and about and the car is off without being plugged in, the 12V battery is fending for itself without help from the HVB like any other conventional vehicle. While plugged in and charging however it will keep the 12V battery maintained as that is key to keeping all the modules including the HVB charging circuitry operational. It will even go so far as to top off the 12V battery after the HVB is completely charged. So leave it plugged in after it says it is done charging so it can do so.