When we make manual backups we typically do so as insurance before applying updates, or to get a copy of a database for testing. We aren’t making backups to contribute to the backup regime, as that is the purvey of the automated backup jobs. The recommendation is to make out-of-band backups as described in the PDF document. An out-of-band backup can be deleted without causing problems and should be deleted when no longer needed.
We don’t (want to) know the particulars of our self-hosted customers’ backup regime, so it’s best that we not affect it, so out-of-band is the way to go.