To update, here is the response from an analyst on this ticket in regards to the backup retention:
cPanel backup will create a new directory based on the current date and then remove old backup directories which exceed the retention time later. This is the safe approach that all backup software should take which ensures that a backup is still available for restoring even if something goes wrong with the new backup. If something fails with the new backup, such as the FTP server running out of space, then cPanel backup prefers to leave things as they were rather than delete potentially important files which can be dangerous.
You simply edit the line associated with the cron job you want to modify the time of. Thus, if you want to modify the time that the new backup script runs, edit the numbers on the line that has the /usr/local/cpanel/bin/backup entry.