The answer is yes.
This is one of the benefits of making a game in a 64-bit, multicore engine.
Everything in the game can change anything else. Now, most things won't have any affect. But let me give you one of the examples:
There's an ambassador you run into as a side-mission that if you help, can change a bunch of other side-quests in the game.
When the quest editor is made available, you will see what we mean in that every quest can actually create new variables that any other quest can do.
This also means that that someone could literally create their own quest, put it up on Steamworks and let others download it that when they go on it, could change something in the existing adventure (which also means, be careful when using third-party mods).