The issue here is the way the original MSI was installed.
If it was installed using SCCM SYSTEM account you won’t have an issue.
In your case it was installed using user account and that’s why you cannot uninstall it using SCCM SYSTEM account, For SYSTEM this application is not installed.
You can try to write a code which is looking how the APP was installed and run Execute-ProcessAsUser to uninstall APP using current user credentials.