A few facts that may help you make a good decision on your setup:
(1) Deform animations only animate the mesh you used to create that animation in Spine editor.
Two separate meshes will not share that deformation. It doesn't matter if they're in the same slot, or the same skin placeholder.
(2) Spine has Linked meshes. Linked Meshes are special meshes that are "duplicated and linked" from an original mesh but can use a different image. If you make changes to the shape of the linked mesh, you are actually editing the original mesh. These meshes are able to share deform animations, but you can also uncheck a checkbox so each can have their own separate deform animations. Linked meshes can be in different skins.
(3) Different meshes can be weighted to the same bones but with different weights.
@MichaelVictor In other words, what you want is what happens by default. Nothing is shared between meshes unless you specifically want to share it.