I have animated my model using Maya humanik with extra bones to control the shoulder pad on my model, the model is exported to fbx and imported into unity using humanoid.
I have masked the bone transform for my extra bone already but when I play the animation, none of the extra bones seem to have animation data
Animation playing in humanoid
animation playing in generic
You need to create another avatar mask excluding all other bones except the shoulderpads, and animate the soulderpads on a different layer (additive) synced to the base animations.
A different setup than I was suggesting, but might be helpful for your setup.
Note this is for an older version of Unity, but is still relevant as mecanim is the same.