Not sure if you have looked at these options from the “Execution mode” section within Automation? There is an option to run the effect once for each group of the modified objects, and the property/properties of each grouping can be configured as well.
With a similar configuration as the one in the screenshot, if your sync can assign the same timestamp value to multiple objects’ “Updated Timestamp” property, then the automation will only run the effect once as there is only 1 grouping identified.