1. I'd imagine that the trigger for that dialogue happens a few seconds after you open the book. (If it isn't I'm sure Larian could tie that to reading the book.) You can remember for a few seconds.
2. I've seen a bunch of examples, and in them, the dialogues seem to happen after the "investigation phase", so to speak is over. There is one that isn't, the love-potion Orc girl, but in that case, "investigation" is identical to "don't kill her".
3. Not everything that is a quest is marked as a quest. On the other hand, not everything has to be a quest. There may be more you can do for the guy's corpse, there may not.
5. Yes, it is bad if you can wipe out the consequences for your decisions. That's the ENTIRE POINT of having decisions in the game at all!
You are not "locked onto a single path from the start". There are probably hundreds of these little decision points in the game, each advances one or another stat incrementally. If you pick Faith + 1 here, you are not stuck picking all Faith++ decisions. You can change to have a "crisis of faith" at any time by choosing one of the other conversation options. Maybe if you do enough of those, and the Kickstarter goals are met, there could be a trait you get for switching your conviction enough.
