The views expressed on this blog are my own and do not necessarily reflect the views of Oracle.
There are database usage patterns, where tables grow big at times and many rows are deleted from them later. InnoDB does never shrink a table space. In these cases we can end up with big data files, which contain a lot of unused pages. It is a waste of disk- and I/O- resources to back them up.
Users have manifold requested that MySQL Enterprise Backup does not back up unused InnoDB data pages. Some want smaller backups, some want less I/O, some want shrinked table spaces.