Happened to mess around with some things, noticed that changing BoneManipulatePosition also seems to affect GetBonePosition, so perhaps it would be possible to do some crutchy thing with taking current angle of a non phys bone, storing it somewhere, setting BoneManipulate position/angles to 0 0 0, then get each vector with bonemanipulate and read its world coordinates through GetBonePosition and assign actual handles like that, and then assign the stored data back, if I worded my idea in an understandable manner.
I'm rather inefficient when it comes to lua (or any scripting/programming stuff), so I'm sorry that I can't help more with that rather than giving some "idea" which may not even work. Although probably you might've already tried that.