@Jake
Invoke-AzStorageSyncChangeDetection should be able to be executed from anywhere you have Azure PowerShell installed. Are you receiving errors or seeing issues when running it?
You could run this command as part of a script in automation, but please note the limitations on the documentation you linked. That said, it sounds like you are trying to use Azure File Sync in a scenario it was not designed for: client-side caching. Azure File Sync is not a client-side caching solution, it's a solution that enables you to cache on a file server. (It's why we do not allow Azure File Sync to be installed on a Windows client - only server.)
There is an existing feedback item where you can add your use-case and monitor for updates from the product team.
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