What if the whole "Good Ending" really was just a huge dream by Quote, who was unable to cope with Curly's death or the destruction of the island, especially after King and Toroko died.
The first decision you can make to save a life is with Booster (shortly after King and Toroko's deaths, I might add). You literally have to skip right over him, ignore him, to further the Good Ending. How would Quote have known to ignore him if he didn't know what would happen otherwise?
After this, he is desperate for a way to carry Curly to safety. So he rips a piece of one of the broken robots out and calls it the "Tow Rope". Then he makes up this idea of a magical mushroom that he supposedly gets from the already-shady Cthulhu.
However, after the repeat of the fight with the Doctor, the dream begins to turn into a nightmare as he realizes that Curly, Booster, etc. are all truly gone. There is nothing he can do to save them. So he descends into the depths of Hell, where he faces off with angels and demons before finally coming to accept all of the death he has faced and waking up.
That's what the words in the Seal Chamber mean. "So hot... the pain..." It's Quote's pain, not Ballos'.
EDIT:
This is merely a way of looking at the whole situation. I personally think that Pixel just failed miserably at splitting the two endings.