Optimized Transform Hierarchy and Ragdolls

I'm attempting optimize the object hierarchy on some models to improve performance, but I'm noticing a problem. It appears the exposed Transforms no longer affect the SkinnedMeshRenderer when they are moved, which breaks the normal method of setting up a ragdoll. I'm looking for solutions to this problem such that I can have an optimized hierarchy and ragdoll support.

Perhaps I could use target matching on the Animator to get it to match the desired ragdoll limb positions? That's seems pretty janky, so I assume there is a more straightforward way to allow bones in an optimized hierarchy to still affect the skinned mesh or an alternative way to implement ragdolls.

Anyone have any tips?