You're right. This is exactly what happened. Paul Johnson knowingly sabotaged his own offense because it wasn't run out of the flexbone formation.
I love the sarcasm, but did you watch the VT game? That's exactly what happened. Bud Foster was geared up to stop his base offense (see the WOLB timing the snap every play) and Paul Johnson absolutely refused to go away from it.
Heck, look at the quote from the Duke game, which we won 38-14: ""I don't know if we ever got into a rhythm. I probably didn't do a great job of calling plays. I think we jumped around too much." I can't find a quote after the NC game, but it was something along the lines of "We can't run our base offense, and we're going to simplify things".
We spent spring and fall practice on the Diamond and Pistol. The Diamond we never saw much of after Duke. The Pistol we rarely saw other than obvious passing situations. This despite some quotes that clearly indicate that our coaching staff told recruits that we would do more of what the Redskins and 49ers are doing.
I really hope I'm reading too much into this and we aren't about to see some sort of mass exodus.