DRV8412: Is there any adverse effect if the PVDD power supply is always on, and the GVDD/VDD power supply is turned on when needed？

Thanks for your question.

See below the absolute maximum ratings from the datasheet. The safe range without permanent device damage for GVDD_X to GND voltage is as per this specification in the table. 

Note, a GVDD undervoltage will be detected if the GVDD voltage falls below the threshold in the datasheet.