Only way to plug the o2 bung is by tuning it out via the ECU. Leave yours plugged in. O2 sensors work in the closed loop section of the fuel map (lower rpms <5k or so). It's basically telling your ECU hey we all good down here or hey I need a bit more fuel. A PC cannot tune this section of the map. The auto tune for PCV will come with a wide band o2 sensor so it can get A/F readings and make suggestions on what to change on the map you have installed. Unless the ECU is flashed, you are locked out of whatever the closed loop section is.
This is why ECU flashes are preferred over PC. However, a good thing about the auto tune would be that you can use it in conjunction with a flashed ECU. So once you have a full map tuned, a PC can read the data and make suggestions given how and where you were riding. You can then load up that map via the PCV and see how it does all the while keeping the fully tuned ECU map as a much better starting point.