Ok, some may disagree with me on this, but I have custom tuned my UTEC with my QTEC cutout, and have logged and logged well over 5000mi of driving and ran the logs through Logmapper.
Your setup sounds similar to mine, in that you are catless either way, and cutout is only bypassing the stock muffler for the most part. While my cutout is right after the turbo, I'm also running an HKS (modified) DP and am catless w/ stock muffler as well.
On my setup, the AFR's do not change enough between having the QTEC open or closed to need a seperate tune to run. I am running 1 map on my UTEC and run both open and closed, and don't see any more fluctuation in AFR than is normally expected between 1 run and another. I think you're seeing such a big difference because of where your O2 is. My O2 sensor is 6-8" right after the turbo, further upstream than yours.
If you think about, the cutout is pretty much acting like a "catback" add-on since you are already catless. Most tuners do not use different 'shelf-maps' depending on whether you have a cat-back or not. Most tuners go by how many Cat-Conv. you have removed to determine which 'tune' they give you. As long as you have a safe tune with the QTEC closed, you should have a safe tune with the QTEC open as well.
Now, if someone were to run the QTEC on a car with cats, and dump was before the cats, then I would think there would be more of a reason to worry about it.