For many applications it isn't a problem to have a common ground shared with the PC, but a common ground is undesirable for test equipment due to the risk of ground loops. You can easily optoisolate the FTDI chip on its I/O pin side, with an isolated DC-DC converter fed by USB Vbus to power the isolated section.
For logic level conversion look at 74LVC1T45 or 2T45 buffers. They support partial power down operation so if you power the DUT side from the DUT, they'll tristate all their outputs if either the DUT is powered off or the USB interface is powered down or disconnected. Powering from the DUT also auto-sets the logic level. Add 50mA polyfuses for robustness.