Disk usage differences Mac OS Extended vs APFS

Why does the backup of my USB drive take up much more space? I have an 8TB USB drive formatted as Mac OS Extended. This is my main backup. The total free space is 3.39 TB. I used Free File Sync to copy the entire drive to an 8TB HD (in a caddy) formatted as APFS and the free space is 2.59 TB. Both drives are fairly new Seagates. I checked the contents with Disk Space Analyser and the folders are identical. I thought APFS managed files better? Is this because of the different physicality of the drives? Should I reformat the APFS drive to OS Extended? It runs primarily from Monterary, while the USB external runs primarily from Sequoia. Thank you.