The good news is that your car charges and drives properly.
There's a school of thought that ignorance is bliss, that all warnings should be ignored, and if the car makes strange noises simply turn up the volume on the radio to drown them out.
Some cars have been driven hundreds of thousands of miles like that.
Agree that you should keep driving but I'd be inclined to plug in one of those small voltmeters into the auxiliary port to monitor your 12v battery to ensure that the dc-dc is consistently providing ~14.3vdc while you are driving and, when you first get into the car and turn the key and before going into READY that the voltage reading is above 12.0vdc.
If anything changes, please do let us know, and wish you luck!