When the pilot ejected is guaranteed that the plane is a total loss. The ejection system triggers a number of things other that the ejection mechanism. All of the secure communication equipment erases itself to prevent it or is key material from falling into unauthorized hands. The plane doesn’t squak its position so that it is harder for someone you don’t want to have access to the plane to find it. Had the plane been lost in territory that the US doesn’t control or that is controlled by an unfriendly country the US wants it to be hard for them to know that the jet is down and where it is so that the US has a better chance of getting there first. The probably can’t be disabled to prevent an, “Oops, I forgot to turn it on” mistake in unfriendly territory and to reduce the risk of it not working.