Is there any way to automatically enable or disable Tracked Changes in a Word document hosted in a SharePoint Online document library? I've tried searching the available actions in Microsoft Flow/Automate but haven't found anything. If there is not any available action in Flow/Automate, is there an alternative way to do it with the 'Send HTTP request to SharePoint'?
As I am not quite sure about your final goal, I will provide some information about what Flow can do.
Just like you said, using call Http request with Rest API we can get the version number of the file. In other words, we can somehow track the document when it publishes a new version. As we shall make the flow be triggered when a file is modified, simply we can turn on/off the flow as your wish.
And here are some examples getting file version number with flow: https://www.glennprince.com/article/creating-a-version-monitoring-flow-in-sharepoint/ https://powerusers.microsoft.com/t5/Building-Flows/Copy-file-to-location-maintaining-version-history/td-p/274223