Unles you're in the team meeting rooms, how can you know what types of offenses they're running? I can't think of one example where a team used 2 QBs, and the coach said that they'd be using the same plays for both. They always tailor what they're doing to the guy who's in the huddle (or attempt to, anyway). BK's no different. Hendrix is still running the spread. He's just being asked to do different things with it than Rees (otherwise, why would he be in at all?).
Again, it's easy to say after the fact, "Well, despite the fact that they were using two different types of QBs, calling different kinds of plays, they were still running the same offense" after the fact when it doesn't work.
And the running the ball thing is a false analogy imo. Running and passing are both parts of a whole. You usually can't have an effective offense that completely ignores either. Subbing QBs is different. For one, I stand by the argument that historically, it usually doesn't work well (didn't say never, just not usually). Secondly, no one player is more important to the rythm of an offense than the QB. Choosing when to run the ball or pass the ball is like a conductor going back and forth between increasing the emphasis of different instruments in an orchestra. But changing QBs is like changing the conductor half way through the symphony. I'm not saying it can't work, but qualitatively it's different.