I’m not sure how that happened. The restore process skips all upload-related code (including rewriting of upload URLs) when you restore a .sql.gz file.
Maybe we are talking about different things? I’m talking about the url column in the uploads table, which usually is //your-s3-bucket/original/... vs /uploads/original on local.
One caveat of restoring a .sql.gz file is that no URLs are rewritten at all. It expects that the server is reachable via the same hostname as the server where the backup was created. You will need to remap URLs if you change hostnames.