I think it is. The saving system in this game is I think pretty linear so I don't think you could backtrack with your new stuff to an old level. So if you want a item from a level, I would assume that you have to finish the mission and continue it from there.
Yea you just want to make sure that you have check marks by Nobody Killed and Ghost for it to count for those achievements. If there isn't one just start over the level again when you're at the result screen and don't continue the story until you get those checks.
From what I got from the strategy guide (answering question 1) it's the first one scenario you mentioned, but I think it only affects the next mission it seems. Meaning even if you got high chaos in the last mission, it's possible to get a low chaos in the next mission and then the game will load a low chaos version for the mission after the one you got the low chaos in. The last mission however takes account of all the kills you've done in the previous missions. So if you killed 50% of total number of NPCs then it factors a high chaos. Magic number for going between high and low chaos is 20%. Under 20% you're in the low chaos. Higher and you're in the high chaos. The type of chaos affects the security, rat abundance, amount of guards, and amount of civilians for the next mission. Can't really answer 2nd or 3rd question since I haven't experimented that much or have the DLC, but the upgrade sequence looks okay to me, but if you prefer to be stealthy and kill only when you need to then I recommend to get Possession maybe? Possession's more for like if you're lazy and don't want to jump around as much, but it's more risky. Max Bend Time is really good for stealth so I'd recommend getting that before Wind Blast.
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