Check to see if there are any differences between the SCCM install and the manual install. For example are different installation options selected, different Property values etc. What commands are SCCM using to install and how does this differ to the manual install?
Try creating a windows installer log to see what is actually failing in the SCCM uninstall - this may give a better idea of what is a happening. https://docs.microsoft.com/en-us/troubleshoot/windows-client/application-management/enable-windows-installer-logging
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