It's not the weight of the trains. That could be accounted for by reinforcing the structure. After all, an S&S 4D coaster train weighs somewhere in the vincinity of as much as a sit-down and an inverted train put together, and it needs only one set of rails to carry the weight.
The "killer" is the dynamics. A train will vibrate and its motions strain the track in different ways, usually solved by making the track flexible so it yields to the forces. But two trains influencing the same track structure simultaneously creates a very complex pattern of dynamic motions, and you can't flex against it since the forces pull in different directions at the same time (just try to imagine how the forces of the wheel bearings change based on the number and placement of riders in each car, for instance). The combined two-train track would get some really wonky strains put on it, increasing the risk of fractures in the long run.
So the simplest solution is to make the coaster as two intertwined - but not touching - structures. That way, they can both flex against their own dynamic motions, without being influenced by the other. Expedition Everest does the same thing. The coaster (influenced by the train), the yeti (influenced by the [former] motions of the multi-ton animatronic) and the mountain (influenced by wind) all have their separate load-bearing structures that don't touch each other, so they don't wear each other out.
I'm not completely sure how Full Throttle solves it, but I'm guessing that it never runs two trains through the loop-hill at the same time. That wouldn't be an option for a duelling coaster, though.
