for now we don't know nothing for sure. wynn if you recover the blade in the pyramid spoke of "a bit of refined power".
for the investment new givini, they became relevant in the successive main quest section, for the rest don't worry, feel free to go everywhere
Adding sx, items or xp once in chapter 4 has little affect to gameplay. If you were adding ProN or changing flags or variables, then yes you would be adding a game bug or glitch that may affect your game's processing of the story.
Well, Sierra did put in some minor "protection" against cheating (for example you can't get Incubus King armor in Deep Pass during chapter 1 if you cheated Simon's level to 40 or higher, or the party Sx to 100k or more). So you might want to be careful and not over do it. Cheating ProN might get you an in-game message from Sierra if you try to invest into something you shouldn't have enough ProN to invest (like Banks in Chapter 2 or Givini dig in Chapter 4).
It's something that happens much later in the game, it's only a temporary thing though.
it's not really a coin toss at all, the fact is the Main guide on the wiki just sucks cause it want's to provide the illusion of choice when there is in fact route optimization.
There is an RPGM save editor floating around somewhere, i'll try and hunt it down.
I wasn't really looking at cheating to advance, just to boost some stats, equip ect. The game itself has a pop-up dialog with a large smiley face and comments from the dev. Which is amusing, but also disappointing since the game is being publicly funded players should do what hey want if they decide to use cheat editors.
it isn't permanent (unlike aka), but for unlock that you need meet some pre requisite, first you need to complete all the research projects of chapter 3 (not the qum's special project btw), and ending the chapter 3 with less of 100 global collateral damage (if you suprpass that sarai asks help to remove the corruption the war trow around the continent).
the discretionary funds is a variable like the pron (sx is the standard currency of every rpgm game). with some high optimizated playthrough you can 'buy' near all the project in the petitions' houses
You can use the walkthrough
You actually do have a choice and there is no such thing as optimized route (there won't be one until the game is completed, and even then there might not be one). Every choice you make have some benefits and some penalties. It's up to you to decide which of those are to your liking.
You can optimize your choices with a save editor. While someone may have gone through the effort of making good choices without cheating, some don't care to play that way and will look for any means to be a fully funded tyrant.
