References are lost and retargeted when a ScriptableObject is cloned with Object.Instantiate in a Player build

How to reproduce:

1. Open the attached “IN-152943” project
2. Open the “SampleScene” scene
3. In the Unity editor, select “File” > “Build Profiles” > select “Windows” profile and click “Build And Run”
4. Observe the "REPRO ORIGINAL" and "REPRO CLONE" lines in "%USERPROFILE%\AppData\LocalLow\DefaultCompany\IN-152943\Player.log"

Actual result: The "REPRO CLONE" line differs from "REPRO ORIGINAL" line
Expected result: The "REPRO CLONE" line matches the "REPRO ORIGINAL" line

Reproducible with: 6000.6.0b6, 6000.6.1f1
Not reproducible with: 6000.0.1f1, 6000.0.83f1, 6000.3.24f1, 6000.6.0b5, 6000.7.0a6

Reproducible on: Windows 11 Enterprise (25H2)
Not reproducible on: No other environments tested