Since when had fighter jet designer stopped caring about Whitcomb's 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?