The scale of your character doesn’t matter, it doesn’t have to be the same size of the Mannequin;
What does matter is the scale of your character relative to the scale of the Mannequin, because it is the base point of reference, get it?!
A Hobbit will be smaller than the actual Mannequin and that is fine; but it must be the correct scale of smaller, relative to the scale of Mannequin in World Space coordinates.
For humanoids you must use the Mannequin’s skeleton, no matter what scale the character is (relative to).
You can change the scale of the rig to fit your character’s mesh, but if you use a custom rig then most likely retargeting won’t work.
You can add extra bones to the Mannequin skeleton, but you cannot add extra bones in between the default existing ones;
Example: Add facial animation bones or hair bones to the head joint, but NEVER add a bone between Neck and Head joints.
You can extend, not modify the skeleton.