"Now do these animated joint centers change based on the rotations of the joint?  If not do they cause the joint to do anything weird at other rotations." 

You could use the dependency editor to tie the joint animation to the thigh bend so that it is kept in the original position otherwise.

Raising the joint centers deepens the hip/thigh gap you get when Dawn does a full 180° side-side split, but it also lessens the balloning of her butt.

The (deeper) gap is easily fixable with some smoothing of the side-side thigh weightmap, so I'd rather keep the joint centers in the new, more correct position, as the default split looks pretty bad anyway.

There is no adverse effect for a normal "legs apart" pose.