If you really need to use features from the Upload extension like download stats but the file cannot be sent, you could upload a dummy file with the same name, then replace the file on S3 manually. You won't be able to edit the calculated file size if you don't have access to the database though, but this is only a visual impact on one of the templates.
The real problem of using FoF Upload with large files on FreeFlarum likely isn't even the upload, it's the download since every file will be proxied through the forum before being transferred to the user as part of the access control and stats. It'll be much faster for everyone to download directly from S3.
