Just to make sure we’re using the same terminology: to put the files in Storj you ran a “backup” in TrueNAS. And now when you said you did a “pull test” did you do a “restore”?
It has been awhile… but I think “Cloud Sync” (using rsync underneath) can dump raw files into Storj-S3. But “TrueCloud Sync” is the backup app (using restic underneath). Both can use Storj-S3 to store their data. If you sent a backup using TrueCloud Sync… but tried to bring it back as raw files in Cloud Sync… I think you’d see what you’re seeing (the restic-named files+directories)