Joints appear at different positions when the prefab is added from a subscene instead of instantiating from the same prefab

Reproduction steps:
1. Open the attached project "ReproProj"
2. Open the “/Assets/8. Joints and Motors/Joints - Single Ragdoll.unity” Scene
3. Pause the Play Mode
4. Enter the Play Mode
5. Observe the gizmos for joints of the spawned entity

Expected result: Gizmos align with the joints of Ragdoll
Actual result: Gizmos are not aligned with the joints of Ragdoll

Reproducible with: 1.2.0 (6000.0.33f1), 1.3.8 (6000.0.33f1)

Reproducible on:
Play mode

Testing environment: Windows 10 Enterprise 21H2
Not reproducible on: No other environment tested