"If they really wanted me to flip, the feature length edit of BOBW would also include the opening of DS9's Emissary in the correct spot."
With seamless-branching Blu-ray technology offers the option of watching multiple versions.
Considering CBS did just one Blu-ray disc with Tribbles for TOS (the TOS and TOS-R episode, the TAS episode and the DS9 time travel episode) it would be a nice gesture to give BOBW
a similar royal treat, at least as an exception from the rule.
In regard to the supposedly "incorrect" framing of "Sins of the Father" I can't possibly find fault with it, especially since it is the only correct framing during this entire BD release that represents the DP's original intentions because he expected the areas outside the safe action frame to be cropped by the overscan of our 4:3 tube television sets, then.
A properly calibrated flat screen with 1:1 pixel mapping or no overscan will display this episode as it had been intended to be seen by the audience.
The amount of time, money and talent literally wasted to clean up production flaws, especially in the top and bottom areas of the images - areas considered expendable by the DP's because unseen by 4:3 TV audiences - is interesting, to say the least.