Reproduction steps:
1. Open the user's attached project
2. Open Assets > BugScene
3. In the project browser double click Variant Prefab to open it
4. Add "OnlyOne" script to root GameObject in the Variant
5. Save and exit Prefab Mode
6. In the project browser double click Base Prefab to open it
7. Add "OnlyOne" script to root GameObject in the Base
8. Save and exit Prefab Mode
9. Observe Variant Prefab instance in the Hierarchy window

Expected results: Variant only has one component of type "OnlyOne", the component from the Base Prefab should be suppressed
Actual results: Variant has components of the same type even though it is not allowed

Reproduced in: 2019.4.31f1, 2020.3.20f1, 2021.1.24f1, 2021.2.0b15, 2022.1.0a12