How to reproduce:
1. Open the attached project
2. Open Main scene
3. Select "GameObject" in the Hierarchy
4. Make a modification to the "Float Array" in the Inspector
5. Notice:
- the field is marked as modified (text is bolded)
- scene is marked as dirty (asterisk by the scene name)
- if you open scene in text editor you will see a property modification is present for floatArray.Array.data[N] with the changed value
6. In the Inspector, right click the modified field and Revert Value to Prefab
7. Wait for few seconds and notice the field reverts to the prefabbed value, but is still marked as modified and scene is marked as dirty
8. Save Main.unity and reload it in your text editor
9. Notice a property modification is still present for floatArray.Array.data[N] but with the prefabbed value
10. Go back to the Inspector and notice that reverted field is bolded
11. Right click the modified field and Revert Value to Prefab again
12. Notice that reverted field is not bolded, scene is not marked as dirty and property

Note: If in step 6 you select component and pick Revert to Prefab, value is reverted but not bolded and scene is not set as dirty.

Issue is not reproducible with nested prefabs