Some unanswered questions.

[Sexbad]

- What was the significance of the rose petals (or whatever flower they were)?

I recall many little blurbs of text and possibly a few flashbacks referring to something tasting of or smelling like Damascus Rose. I believe it is the amnesia drink that has this taste, so the petals are symbolic of the past he is trying to forget.

- Why does the Shadow leave Daniel alone in the 'revenge' ending?

The Shadow seems to be set back in its attempts to kill Danny as he kills others. Perhaps killing Alex, considering he's one powerful motherfucker, was enough to nullify the Shadow. Or, since the Orbs definitely had influence over the Shadow, Alexander's pursuit to get Orbs angered It and Alex's death was enough for Daniel to be left alone.

- Why did a naked corpse suddenly spawn into existence on a bed frame in front of Daniel in the prison cell area near the end of the game (after Daniel breaks out of his own cell)?

It's not a really big deal plot-wise, but I believe it was supposed to be a reminder of how much of a dick Danny was being, considering he tortured a bunch of people. The nakedness, I think, is also supposed to serve as a sort of reminder of how defenseless you are. It's all symbolic, not particularly meant to be focused on how it got there.