I exchanged a couple of emails with Wayne of the subject. He recommended leaving the O2 sensor engaged. Since it only effects the mixture in closed loop there is no risk to the engine. Having watched the transition to open loop on my Scangauge, its obvious that any aggressive application of the throttle will immediately switch to open loop and the Tuneboy tune takes over.
Having run both ways, the only difference I noticed was slightly better fuel mileage with the O2 sensor connected. Wayne made no mention of the ECU overwriting the tune.
Also, if you're going to disable the O2 sensor in Tuneboy you need to either remove the sensor or install the Dynojet part to bypass the sensor. If you do neither it will receive no power and will be damaged in short order. Not a big deal as long as it is disabled, but it will not function should you want to enable it at some point down the road.