There should be two options when coping S3 tables with mysqldump (should be a startup option --copy_s3_tables, boolean, default no)
1) Ignore all tables with engine S3, as the data is already safe in S3 and any computer where you restore the backup will automatically discover the S3 table.
2) Copy the table as a normal table with the following 2 changes:
- Change ENGINE=S3 to ENGINE=ARIA;
- After copy add to log 'ALTER TABLE table_name ENGINE=S3'