YOU have been conned. The stadium clock is Not Official. This is why the conference is challenging the outcome of the game.
I officiated high school and college football for over 25 years. I think I know what the official clock is and it's the clock on the primary scoreboard. You obviously misunderstood what the explanation was by the Big 10. The issue is with how the replay cameras are synced to the stadium clock. All the video cameras are supposed to be synced to the stadium clock before the game. There is a technical problem that causes the main TV camera that superimposes the first down line on the screen to fall about quarter second behind the other cameras. That's why the main camera showed the clock hit 0:00 before the pass was touched out of bounds while the end zone camera showed there was still 0:01 second on the stadium clock when the ball was touched. While the end zone camera was probably the more accurate one, the replay protocol dictates that the main broadcast camera is the one that should be used when determining timing issues such as this. The reason for that is obvious. The main camera is the one everybody looks at. Had they followed the protocol, they would have made the ruling based on what the main camera showed. Nobody would have ever known what the camera in the replay booth showed and there would be no controversy. The ruling on the field that the game clock had run out during the first Hail Mary would have stood and Western Michigan would have the victory.
The NFL has a protocol that says even if replay shows the play ended with one second still on the clock, they do not put time back on the clock. If it's that close, the call on the field stands and the game is declared over. If there isn't at least a two second error, the play stands as called on the field.