It's fundamentally different because the loss was some what controllable. They could have won and gone undefeated.
Losing puts a team at the mercy of more tie-breakers. Sure that sucks, just not as bad.
In the 3 Undefeated scenario, one of the teams is going to get left out when they did all the could to get in the Title game (winning every Conference game). To me that is much worse.
On the other hand, if that team still gets to go to the NCAA Playoff and host a home game, then they are probably good with it. Rest up.