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This would depend on the flow action or what you want to do with the smart lists. If you have a large smart list for sending an email, I suggest you use Email head-start. Also, Marketo would be dividing the list into small batches when sending the email via throttling.
If you want to change some data value, it should be done in batches, since it can slow down your other marketing campaigns as well as the sync between Marketo and Salesforce.
I'd agree that this is best practice. Some larger organizations use spam filters that if they are pinged by one IP address too many times they will block the email as a whole, so throttling the email send makes sense.
If you are making an email update and you don't need to immediately trigger an update you could look at batching updates over night rather than during business hours to make sure your system isn't slowed down too much.