Reproduction steps:
1. Open the attached project "ReproProj"
2. Open the “/Assets/SampleScene.unity” Scene
3. Open the “/Assets/SampleScene.unity” Scene file in IDE
4. Look for “m_Modifications:”
5. Observe that it has 6 properties
6. Remove those properties and replace them with “m_Modifications: []” and save
7. Refresh the Editor for the popup to appear, and click “Reload“
8. Change anything in the Scene for it to appear dirty and save
9. Undo changes and save again
10. Observe the Scene file in the IDE

Expected result: “m_Modifications“ is not overridden
Actual result: Properties for “m_Modifications“ are overridden

Reproducible with: 2022.3.62f1, 6000.0.51f1, 6000.1.7f1, 6000.2.0b5

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

Notes:
- Properties can’t be edited in the Editor directly
- The driven RectTransform system serializes these properties always as zero to prevent unnecessary changes in version control, however, it still clusters the Scene file
- The RectTransform of the Canvas GameObject is being driven by its Canvas Component, which doesn't cause these Prefab overrides