We haven't started work on this yet.
But for what it's worth, BoundingBoxFollowers are independent of the SkeletonUtility system. They will work with SkeletonUtility or BoneFollower or with any other component you come up with.
So if it's just two or three bones, using BoneFollower would be fine. SkeletonUtility is still the way to go if you inevitably have to follow several bones related to each other in the hierarchy.
It's definitely an execution order problem, though it doesn't matter what Unity version it is. I was able to replicate this problem in Unity 5.6
The current workaround for ensuring the correct update order seems to be just to disable and enable SkeletonUtility one frame after SpineRootMotion has the chance to initialize.
Currently, our components don't have the APIs to ensure event order so changes to make this cleaner would need to be done in the next version of Spine-Unity. We can do this in 3.7.