There are several considerations:
1. Really heavy engines affect the balance, by affecting the location of the center of mass of the aircraft. That center of mass needs to be located near the center of lift, otherwise when you apply lift at the forward end with the wings and weight at the aft end with engines, the plane will tend to pitch. With aft mounted engines, the wings are usually mounted further aft on the fuselage (e.g. DC9, DC10, L1011) to move the center of lift back near the center of mass. But with really heavy engines, you are better off just mounting them under the wings, which eliminates most of the balance issue immediately.
2. Engines that are mounted low beneath the wings are more prone to foreign object damage than those mounted high on the tail. On the other hand, engines mounted on the tail are more likely to ingest water kicked up by the landing gear.
3. Engines that are tail-mounted can have certain flight maneuvers that create severe inlet distortion. For example, a side slip at a high angle of attack may result in the airflow to the engine inlet on the "downwind " side being functionally blocked by the fuselage or the wing ahead of it. This can cause compressor stall and temporary loss of thrust at a critical flight condition. Since wing mounted engines generally have inlets ahead of the wing, this is not a serious issue for them.
4. Not sure I understand the earlier statement about applied moments. The truth is that engines mounted beneath a wing will create a huge bending moment on the wing structure as thrust is applied. That's because the engine center line is well below the mounts, and even further below the wing structure that holds it. Tail mounted engines are mounted so close to the fuselage center line that bending moments, while still present, are greatly reduced.
5. (Added) Finally, wing mounted engines result in a much quieter cabin than tail mounted engines, which tend to place that screaming fan right next to the aft seated passengers.
So it's a tradeoff, like most things in aircraft design. Structurally, tail mounted engines are probably easier to deal with. From an aerodynamics, flight control / stability, and noise standpoint, I would guess that wing mounted would be more favorable. And once the engines become large enough and heavy enough, the balance issue simply will not allow a tail-mounted version.
ADDED (2): Your concern about flow under the wing is valid, but the only disturbance that is really created (once the aircraft is moving) is the relatively narrow strut that attaches the engine assembly to the wing structure. That's not a huge effect.