Overwrite is the best import option to ensure the data extension only contains currently active customers, as it deletes all existing records in the data extension and replaces them with the new records from the import file.
This ensures that only customers who are included in the daily feed remain in the data extension. Append or Add and Update would not work for this scenario, as they would either add new records without deleting old ones or update existing records without deleting old ones.

Send throttling can help NTO achieve this send while keeping deliverability metrics in mind by limiting the number of emails sent per hour to each ISP or domain. Einstein Engagement Frequency can help optimize the send frequency for each subscriber, but not for each ISP or domain. Sender Authentication Package can help improve sender reputation and email deliverability, but not address the issue of sending a large volume of emails at once.