Bone and attachment (Images) compensation affects manipulating bones in the viewport. It does not affect applying constraints. It is not applied when adjusting a transform constraint.
You are fine up to this step:
If I understand, you parent the slot to the root bone, apply the transform constraint, then parent the slot back. That puts the arm in the right position, but in your original skin the arm moves. Is the arm that moves in the same slot? If so, then you can't use parenting the slot to the root to move your attachment. Instead, parent only the attachments in the second skin to the root bone in a new slot, apply the transform constraint, then parent them back and delete the temporary slots on the root bone.
As a simpler test, instead of changing the parent of attachments in the tree, just manually move the attachments to be in the right place in the viewport. Each attachment has its own position. Moving one doesn't affect other attachments in the slot or in other skins. (Except for linked meshes, which share the vertex positions.)
For your IK scaling problem, you probably need to set the transform constraint to local and possibly relative. In general it's not possible to tell what is going on from an image or GIF. If you can send a .spine file it would be easier to provide guidance.
