Tool is not detecting conflicts in prefab instances

How to reproduce:

1. Download and extract the user-attached “bug.zip“ file
2. In each of the provided example directories modify the command in the CommandLine.txt file by doing the following:
   1. Replace the Editor location with the Unity Editor's locations on your machine
   2. Replace all the instances directing to “mergebug.log“ and the test prefabs to the extracted folder’s specific example’s location
3. Run the commands in each of the “CommandLine.txt” files
4. Check the generated “mergebug.log“ in each of the examples

Expected result: The log should have a conflict in all three cases
Actual result: The result prefab has both modifications in all three cases, and the log shows no conflicts. In the component case, it adds the component twice

Reproducible with: 2019.4.39f1, 2020.3.35f1, 2021.3.4f1, 2022.1.4f1, 2022.2.0a17

Reproducible on: Windows 10

Notes:

1. When using a VCS, the system does not detect the conflicts properly when two or more users modify the same prefab instance
2. All the modifications are stored in the YAML and executed when deserializing the asset. Making only the latest to be persisted or displayed, but it never identifies this case as a conflict