Decided to publish an example for a multiple pathway mission through triggers. There are 2 different ways to solve the mission, and you have different ending text as well. Unfortunately you can't tie in the branching dialogs yet. The NPC default dialog doesn't have Component complete triggers and the map dialogs are bugged.
It is a Fed mission called Branching Story Mission.
It's a nice try which may encourage immersion in a map, but we still need more support from the tool-set because checking out the mini-map and not finding any points of interaction, or not having any objectives that lead the player down a path may prove to be too much for some.
The lack of blinking items are just my fixation with invisible objects because it reminds me to the old point and click adventures. You can easily add blinking consoles, too. Anyway, this should be used carefully because the average player can get helpless very easily.
The whole idea rests on blocking the access to a story element. The main problem is that there is only 1 way to turn off an object (there is no OR branch in the state change) so you need multiple blocking objects.
The more individual blocking objects you have, the more parallel OR branches you can add.
It is not really messy. You just have to name the triggers logically.