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I have a flex fuel kit using the rear O2 sensor input as well as boost control through CPC/EVAP and all of my emissions monitors show up as ready. I think as long as the flex fuel programming in the tune is set up correctly, the monitor will show as ready. The expected range of the O2 sensor should be adjusted to cover the expected range of ethanol content, so you would never fail a range check and end up with an value out of range code.
If for whatever reason, it does not show up as ready for you a few hundred miles after flashing, you could ask for a secondary file without flex fuel and simply reconnect your OEM rear O2 sensor while running 100% pump gas.
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