Hi,
I think it’s important separate discussion from creating bones for Control Rig and creating bones for Skeletal Mesh.
Bones in Control Rig do not depend on Skeleton asset, they can be imported from a Skeletal Mesh and create a weak reference to it, but once they are in, they are treated as separate set. It means they can be modified, renamed, restructured etc. and it won’t affect the original Skeleton asset or Skeletal Mesh from which they were imported from. (other than Control Rig may stop working on Skeletal Meshes using that Skeleton because hierarchy wouldn’t match).
As far as I know, in unmodified UE5 there is no way to add normal bones to Skeletal Mesh. Virtual Bones act a bit differently and do not support many features that normal bones do. It also seem not possible to remove bones from SkeletalMesh asset for good, but removing them from a LOD level is possible. (effectively removing the bone and moving all weights of it on vertices to other weighted bones)
Hope this clarifies things a bit.