Some unanswered questions.

[Zopy]

- 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)?

As others have suggested, I think this is a sanity based thing. I remember once in the main room of the transcept, the ceiling was clear. However, I went into a torture chamber, and my sanity lowered dramatically. When I came back, there was a corpse hanging from the roof.

As for the appearance of the corpse in the cell, I think it's the same idea, except scripted into gameplay so that it always appears.