When we perform a retarget from an input pose rather than another mesh, the transforms within the anim bp have already been conformed to the target mesh by translational retargeting and compatible skeletons. When translational retargeting is disabled on all of the mesh's bones, and the ref poses have the same bone orients (so compatible skeletons doesn't come into play), we still get different results because the IK retargeter only has access to the target mesh's retarget pose and not the source. You can see this in FAnimNode_RetargetPoseFromMesh::EnsureProcessorIsInitialized where the source and target mesh components are the same.
If we supported a property on the retarget anim node that allowed users to specify a different mesh for the source retarget pose, it would at least fix the situation where translational retargeting is disabled and there was no compatible skeleton fixup.