How is the center of mass controlled in planes with multiple tail engines?
The wings are placed sufficiently far aft.

Yes, moving the wings aft moves the C/G aft as well, but since the fuselage has some weight, eventually the centre of lift overtakes the centre of gravity and there you place the wings.

A slight problem is that C/G of cargo gets quite a bit ahead of the C/G of the airframe, causing a large difference in overall C/G position between empty and loaded aircraft and a larger horizontal stabilizer is required to maintain control over the whole range. And that, of course, reduces overall efficiency.

When you look at aircraft with tail-mounted engines, you'll see that it has wings further aft compared to one with wing-mounted engines.

Note that Concorde additionally could transfer fuel between forward and aft fuel tank in flight to adjust the C/G in flight to reduce the needed deflection of the elevators. But that was not because of the overall aft C/G—the centre of lift was correspondingly far aft—but because the centre of lift moves quite significantly aft in supersonic flight.