We don’t have a way of doing this from PYNQ as it’s a bit risky to be poking the power regulators from a multi-process environment without dedicated driver support that we don’t have. It’s theoretically possible to bash the I2C bus from user-space but that risks frying the board without extreme care.
On the ZCU104 the PYNQ image should during the very early boot stage interrogate the FMC card and set VADJ appropriately. If you want to override this the best bet is probably to patch that part of the FSBL. This part of the boot process is built on top of Petalinux so you can follow the guides on patching the FSBL with xfsbl_board.c being the file of interest.
Hopefully this is sufficient to get started.
Peter