How to reproduce:
1. Open attached project "New Unity Project.zip" and scene "SampleScene"
2. In Hierarchy window, expand "Root" object and select its child "Nested"
3. In Inspector window, GameObjectReference(Script) -> press on "Part of Root" (this highlights the "Part of Root" in the Hierarchy window)
4. In Hierarchy window, do "Unpack Prefab" for "Root" prefab
5. Enter Play mode
6. Repeat steps 2 and 3

Expected result: the "Part of Root" object in the Hierarchy is selected
Actual result: nothing is being highlighted, double-clicking on the "Part of Root" in the Inspector, opens up "Root" prefab

WorkAround: Apply the reference to prefab after the outer prefab was unpacked (this will not change the asset because the link now points to scene object and preserve the link to scene object).

Reproducible with: 2018.4.28f1, 2019.4.13f1, 2020.1.10f1, 2020.2.0b8, 2021.1.0a1