I don't know if it's possible to dump headers via cybergadget/powersaves. I know that the rom uses a different clock frequency than the save chip for games that have dedicated save chips. I do not know if Pokemon XY carts are an exception to this.
These clock frequency differences prevented using R4i Savedongle devices to dump 3DS roms. I made a post about this a few years ago. The same may or may not apply to other hardware dongles.