My guess is that there were meant to be more routes where you'd save these same people once each under varied circumstances, but reduced work time forced the devs to cut and compress things.
WMG / It Came From The Desert
The reason why the TurboGrafx-16 version feels so disjointed? The devs got screwed over.I dunno about that version's development history, but it feels like they were pressed for time. There's multiple instances where you have to rescue the same characters from the Antmind, and cutscenes have a tendency to contradict one another (not to mention the infamous phantom transponders).