There's a difference between civilian transponders which generally squawk all the time and military IFF, which typically only responds to a coded challenge (called an IFF interrogation). If a military IFF doesn't receive a valid interrogation, it remains silent.

It is Very Bad if an enemy can either spoof a valid "friend" IFF response or cause IFFs to respond and give up one's position. The latter was done with great effect in both WW2 and the Vietnam War.

That's easy. On many civilian planes, beacon turned on automatically, but on military must be turned on intentionally.

Because of this, extremely typical, when you see military plane, but have not got alarm about it's approach - just pilot forgot to turn on beacon.

FoF system is totally another measure, in real dogfight they do not consider it much, it is mostly like additional spare fuse, may save your life in some case. Rumors said, pilots of U-2 was pray, to avoid cases, where need to use these radio tricks.