I read in another thread that when Winona examines the shadow atrium, she says how Charlie used to have such a big heart. To aquire the atrium, you have to complete the marble pieces and break them open. Maxwell states that while he did create the mechanical pieces, the statue versions were not his making, so it must have been Charlie. Once you kill all three and get the heart, you use it on the skeleton to spawn the fuelweaver. He's strange because his dialogue implies he's just trying to save you in preventing the portal from reopening. It seems his empathy is the heart's doing. While the heart is a source of immense darkness and ferocity, it also seems to have a great deal of compassion as well. After the fuelweaver is defeated, "They" take its heart back (meaning you have to retake it from the shadows) and a rose is dropped signifying Charlie yet again.
I think that the reason Charlie is able to use the throne without being bound to it is that she no longer has a heart, unlike everyone else. "They" took it as some sort of deal with her.