Is there a downside on using APFS on a conventional HDD when using macOS 10.13 or later?
Yes there are downsides to HDD formatted APFS instead of HFS+
The newer format is optimized for solid state characteristics.
The older format is optimized for HDD characteristics.
Unless you are sure you need the new features, stick with the format that’s best for your storage type. If you don’t care about long term performance or use the storage lightly, it can be fine and not even measurable but heavy use will cause you to wipe and reformat the HFS in my experience if you choose and use APFS for months of continuous use on HDD as the inefficiencies build up over time and the storage allocation cannot self-optimize like HFS does on HDD.
My advice: Use Time Machine if you only have HDD to back up or provide SSD storage to Super Duper.