If you're not planning on using the built in Time Machine functionality, then you should format your backup drive to whatever the source is. So if you're backing up an APFS source use an APFS backup.
The only reason that solution doesn't work for Time Machine is because of how time machine uses hard links which APFS doesn't support, so in that case the time machine drive needs to be HFS+.
I have both SuperDuper!, and Carbon Copy Cloner, as well as the built in Time Machine functionality of the OS.
All good solutions with their pros and cons.
The only other time I would recommend against APFS is:
1. you plan on using software not compatible, such as an older version of the macOS.
2. or you backup solution doesn't support it.
Now that you have Mojave, and your Fusion drive has been converted to APFS, you now have snapshots right on the system drive, so if you need to roll back, you can do it now right from the system drive. (similar to Windows restore points.). Keeping an external backup now, is just a way of having the content backed up to another source.
I'm sharing this, because if you were to have something happen to the external backup. APFS would still have a backup from the last 24 hours. It does a snapshot every hour for the last 24 course. So you should always have a current backup of the last day on your APFS drive.