While I appreciate the thought going into the flaps, it violates the K.I.S.S. principle: Keep It Simple, Stupid (no offense!).
I don't know what sort of traffic conditions you have to deal with, but especially if I'm in busy multi-lane conditions, I want to be able to glance around at any time, with no notice, without reaching for a button or something.
I'm recalling the PNGV cars and how Chrysler's version had a more vertical visibility panel. It appears to me the flow is designed to skip over the rear window and reattach on the decklid. The car had impressively low Cd; right in there with the Ford and GM models, so that break in the flow must not have had negative effects on drag.
Also I wonder why you are proceeding on Version II before knowing how Version I actually performs, i.e. "I wonder if the angle is too steep and flow is separating". A yarn test on VI would answer that.
Lastly, there is no gaslog data for us to peruse. There is no way of telling how effective this device is for improving fe at all.
Anyhoo, feel free to proceed and let us know how it works out.