Yes, actually Skeleton Layer (I mean traditional Skeleton Layer, not Skeleton Deformation Layer) does nothing. This is just a “container”, which stores a list of Bones. Bones are just a global objects, stored in Synfig file, like Exported ValueNodes.
You can learn about Exported ValueNodes here:
Unlike Exported ValueNodes, Bones are not displayed in Library Panel.
Bone defines a transformation. Each Bone also may have a parent Bone and in this case its transformation is a combination of its own transformation and all transformations of parent bones.
You can attach any parameter of any layer to Bone, by converting that parameter to
Bone Influence convert type.
BoneLink is used when you want a parameter to be influenced by one bone.
Bone Influence is used when you want a parameter to be influenced by multiple bone (with weights).
So, when you are linking a group to Bone. Synfig converts Transformation parameter of a group to
BoneLink and sets selected bone as its “Bone” parameter.
So, what you will need is to calculate transformations for parameters affected by bones. Maybe this is possible to do using Lottie’s expressions, but I do not know much about them.