I kind of like the idea. Imagine some of the crazy stuff you could do if you put someone like Cobb or someone else with legs and an arm behind center unexpectedly. I'd imagine in some cases you'd make your opponent burn a time out, in others it'd just be fun to see.
However, I think the idea behind this is player safety. If your #2 QB goes out due to a possible concussion the league wants to avoid a situation where a team needs to decide between having a complete evaluation of the player and forcing the team to use their #3 for the rest of the game regardless of the results, or risking more damage to put the team in a better position to win.