Not sure I understand the 3rd QB thing...there is no positional limit on game day rosters now, is there? IE: If a team wants to have 4 or 5 Qbs on their game day roster they can.
There has to be more to the rule
It keeps a non QB from playing the position and for safety reasons. SF put Purdy out on the field when he was still hurt. No one was trying to intentionally injure him further but a freak accident and who knows what happens. It prevents those situations from happening and I'm sure the owners/league wasn't pleased seeing ratings go down for the game when McCaffery had to play QB. At It may not been a lot of hope but remember what we did in Mirace at The Meadowlands 2.