How is the area rule applied on airliners like the A380?
First of all, not the area should be equal, but the area gradient along the direction of flow should be shallow. The minimum drag with a given volume can be achieved when the area distribution is that of a Sears-Haack body. Ideally this rule applies only at Mach 1, and once you go faster, the cross sections which matter are those along a Mach cone, not those of the aircraft's cross section.

For subsonic flight, the penalty for neglecting the area rule is small; it only matters when local flow is supersonic ahead of a contraction of the contour of the aircraft. Subsonic flow would decelerate, whereas supersonic flow will accelerate further and result in a drag-intensive shock downstream. Adding something to fill up the contraction will reduce the pressure gradients and ideally avoid the shock. By this, area ruling will help to shift the onset of the Mach-related drag rise and enables airliners to cruise a little faster. Honestly, I cannot see the "obvious" area rule shaping on the A380 - to me this is classic subsonic aerodynamics which tries to avoid sharp pressure gradients in the area of the wing airfoil's rear loading. Especially the outer engine pylons could be done better, but I digress.

For airliners, it is much more important to have a constant fuselage cross section, which makes stretching the fuselage simpler and is much easier to build. Area-ruling the fuselage simply is not worth it (yet) when your maximum cruise speed is just Mach 0.85. It is enough to add some Küchemann bodies to smooth out pressure gradients.

Below is a comparison of a swept wing at Mach 0.9, on the left clean and on the right with Küchemann bodies. Note the massive flow separation on the left wing, whereas the flow pattern on the right wing shows attached flow.



Mach 0.9 wing comparison (picture source)