@Snowden, this is due the fact that the hierarchy from the animation only skeleton does not really have any relevance to the animation. There’s no reason to define it as a skeleton if there is no mesh to drive with it. However, you still get the benefit of the transform names as the targets of each animation curve. This means you will go through each curve in your animation and find the name of the corresponding bone in your defined skeleton and replace the target of the curve with your skinned bone. This is another thread in which I talk about retargeting animation only files with a code example for doing so on a biped rig.
Our animation systems are undergoing some improvements right now and simplifying retargeting is in the cards, but I have no eta when we will have it all in and ready for consumption.