I guess you are correct in that the RigidBody does not have a hidden pin for the bone setup (where scale would logically be), because it just uses the PHAT asset.
Could you possible have messed something up inside your PHAT asset?
IF not, Try calling a ResetDynamics on the mesh Anim Instance whenever after the scaling.
IF both fail, file a bug.
Switch to an Anim Dynamics node. See if that helps.
The difference is you have to manually set up the chain and it’s constraints within the node.
To pass your own scale (which by the way is insane. you should not need to)
You have to resort to a FABRIK or IK node of some sort.
Oh, and ofc, you can always ModifyBone to apply the scaling BEFORE the rigid body node.
Insane as it may be?