According to this source, designers of military fighter jets seemed to have stopped centering their design on Whitcomb's Area Rule for quite a while. Yet even the twin series fighters struggle to break the sound barrier without afterburner in a combat loadout. Then why have the designers stopped caring about transonic drag reduction? Or is it because they never intend to let their jets come near Mach 1, just a little bit below it or use the afterburner and shoot past it? Does this mean newer supercruising fighters, if they intend to fly all the way up to their Mach 1.5-ish cruise speed on dry power, should still care about shaping according to the Area Rule?
Of course designers still care about the area rule, but it has become less important. The original area rule is just for Mach 1; at higher speeds you need to look at the cross section distribution along the Mach cones - but which ones? They change with angle of attack and Mach number, and there is no single point anymore where performance needs to be optimized. Rather, the aircraft has to perform well from subsonic to mild supersonic speeds, and the higher speeds for which the older designs from the Fifties and Sixties were optimized turned out to be irrelevant in practical use.
Next, which configuration needs to be optimized? The F-106 carried exactly one type of AA missile. Today, the typical aircraft will carry everything from dumb bombs to laser illumination pods, with fuel tanks and electronic warfare pods thrown in between. With that kind of variety in accessories who can tell which configuration exactly it is which needs to obey the area rule?