Fantastic catch, Dras. The FAQ has precise rules about the meaning of "set aside" squadrons, and how in-game deployment of these squadrons works. Even if the expression is only clarified in the context of Hyperspace Assault, it's a pretty solid basis.
EDIT: It's worth noting that the new Fighter Ambush objective card also involves "setting aside" squadrons. Presumably all instances of "setting aside" will be resolved the same way unless otherwise specified.
If we do accept that, then we accept the follow on: As these are inevitable questions that, also, are not answered by the Card ..... But we can find guidance in the FAQ:
If all of a player’s ships in the play area are destroyed, his ships and squadrons that are set aside are also destroyed.
If the game goes to time, or the end of the sixth round, his ships and squadrons that are set aside are destroyed.