MessageStats has module to work with Exchange Online. Office 365 is supported and you can use the module to get reports from your Exchange Online.
For the newest version of the software a module has been designed to provide access to the M365, Exchange Online.
Here is the link of the documentation that will provide more details of what is required:
https://support.quest.com/technical-documents/messagestats/7.8.1/release-notes/2#1056248
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