@Jon Mercer, Thanks for the reply. For the CMTrace tool, it is one tool of Configuration Manager. Currently, based on my research, I didn't find it can download directly on the official document. To get this, you can download the Configuration Manager from the Evaluation center:
https://www.microsoft.com/en-us/evalcenter/evaluate-microsoft-endpoint-configuration-manager
Then you can find the CMtrace.exe after unzip the install file:
https://learn.microsoft.com/en-us/mem/configmgr/core/support/cmtrace#locations
For our Intune issue, I notice the script needs to be run under system account. To manual test on the device with system account, we need to use PsExec tool
https://learn.microsoft.com/en-us/sysinternals/downloads/psexec
For log analysis, it will be a little complex, You can consider opening case to help you in a more efficient way. Here is a link with the steps to open case for your reference:
https://learn.microsoft.com/en-us/mem/get-support
Hope it can help.