Reproduction steps:
1. Replace "mergespecfile.txt" in <Earlier version directory, ex. 2019.4.10f1>/Editor/Data/Tools/ with attached "mergespecfile.txt"
2. Upload attached "Prefab-Reorder_ORIGINAL" (built with an earlier version of Unity, ex. 2019.4.10f1) to GitHub repository via TortoiseSVN
3. Checkout two versions of the project, CheckoutA and CheckoutB via TortoiseSVN

4. Open CheckoutA project with the later version of Unity (ex. 2019.4.24f1)
5. In Project window, open "TacticalUICanvas.prefab" in Prefab edit mode
6. In Hierarchy window, select "AbilitiesModule" GameObject and open it in Prefab edit mode
7. In Hierarchy window, select "UIPCHotkey (1)" GameObject
8. In Inspector window, modify the RectTransform values for Pivot.x from 0.5 to 0
9. Save the changes, close the project and commit changes to TortoiseSVN

10. Open CheckoutB project with the earlier version of Unity (ex. 2019.4.10f1)
11. In Project window, open "TacticalUICanvas.prefab" in Prefab edit mode
12. In Hierarchy window, select "AbilitiesModule" GameObject and open it in Prefab edit mode
13. In Hierarchy window, select "UIPCHotkey (1)" GameObject
14. In Inspector window, modify RectTransform values for Rotation.x from 0 to 45
15. Save the changes
16. Using TortoiseSVN, attempt to update CheckoutB with the changes made in CheckoutA

Expected result: No conflict
Actual result: Conflicts when trying to merge the .prefab files

Reproducible with: 2019.4.10f1 -> 2019.4.24f1
Could not test with: 2018.4.34f1, 2020.3.4f1, 2021.1.2f1, 2021.2.0a13 (console errors break project when trying to modify prefab)