The automation emails are combined into one thread because the subject title does not change except for the account name. So even though the recipe is different they are all grouped into one thread.
It would be very helpful if the email subject was the name of the recipe being run instead of "Rule Engine (account name) Report". It should be "Bid to Target ROAS (Keywords) (account name) Report". Attached is the suggestion visually explained.
We have updated the subject of automation emails to include Rule Engine strategy name in it. This should help you identify them easily.