When you talk about reimporting the keys, are you referring to Unreal? What’s your process for getting the joints exported? You mention baking, so I’m not sure if you’re using the Export Motion tool or not.
Chains definitely don’t need to be children of the root. We have characters on Paragon with tons and tons of chains and leaf joints everywhere.
Are you trying to import an FBX as mocap using the Import Motion tool? If that’s the case, then I think I added a change some time ago where importing mocap on chains and leaf joints required the user to select those controls before importing, as it was requested from our animators here.