That setting downloads the files to a temporary directory and includes them in the backup. It does not put them in the uploads directory. To get them in the uploads directory you need to restore the backup. I would do it on a new server so that if anything goes wrong your original server is still intact.
It sounds like some files may be missing. Do you have posts with missing images? Another possibility is that the uploads table includes uploads that are no longer referenced on posts, so those missing images don’t matter.
If it’s only 100 or so then it likely isn’t that big a deal.
Or it could be that a bug at some point cleaned up (deleted) files that should have been kept.
To see the files that it downloaded you’ll need to download the backup file and see what it includes. Restore your backup to a new server to see how it works.