Look, Zimmer is not the first to use this structure. If you ever heard 1942 by Vangelis, for example, you would notice the same structure was implemented.
The reason is merely emphasizing different cues throughout the soundtrack. Notice the difference between tracks 11 (Reunion) and 12 (Slaves to Rome) on Gladiator. Each one of them has a main and different cue. The continuity motif has an added value to the wholeness of the track. This is not an easy task, and therefore delibiratly applied.
You should at least appreciate the good work Zimmer did in The Last Samurai as well as in Gladiator and MI2 (and Pirates of the Caribbean, composed by Badelt at media ventures).