It's not an issue for PIO-USB, since the pullup/pulldowns in USB are just used for device and speed detection. And for the pulldowns to do anything the pins have to be high impedance which you can't do in PIO code anyway. So just making sure to drive the pins low for 1 cycle before putting them in high impedance mode is sufficient as a workaround.

Could be an issue for logic analyzers, though usually you'd have a voltage translator in front of that anyway.