Reproduction steps:
1. Open the attached “ASDQWE” project
2. Open the “Assets/Scenes/SampleScene.unity” Scene
3. In the Hierarchy Window, enable “PhysXAuthoringSubscene” Subscene for editing
4. Open the Entities Hierarchy Window (Window > Entities > Hierarchy)
4. In the Entities Hierarchy Window, select Runtime data
5. In the Entities Hierarchy Window, select PhysXAuthoringSubscene > CubeWithJoints > CubeWithJoints GameObject without the prefab tag
7. In the Inspector Window, observe the Physics Joint > Body B From Joint > Position“ property X and Y values
8. In the Entities Hierarchy Window, select PhysXAuthoringSubscene > CubeWithJoints > CubeWithJoints GameObject with the prefab tag
9. Repeat the 7th step

Expected result: The property values are the same and are equal to 0
Actual result: GameObject with the prefab tag has “X” and “Y” values different, resulting in a discrepancy from the GameObject without the prefab tag

Reproducible with: 1.0.8, 1.0.16 (2022.3.10f1)
Could not test with: 1.1.0-exp.1 (“error CS0006: Metadata file 'Library/PackageCache/com.unity.ext.nunit@2.0.3/net35/unity-custom/nunit.framework.dll' could not be found” errors)

Reproducible on: Intel macOS 13.5
Not reproducible on: No other environment tested

Note: Not reproducible with Unity Physics Joint authoring components