This is by design. The Joomla! site's files and database are always being backed up. I have planned two features which will let you work around that:
1. The ability to assign the root directory and main database of the backup. This pretty much allows you to backup an external PHP application without backing up anything from Joomla! itself.
2. The ability to skip databases during restoration. This allows you to backup external applications even without the first feature, as well as perform partial restorations of a multi-database backup.
The first feature is planned for Akeeba Backup 3.3.b2, to be released towards the end of Q2 2011. The other one is planned for Q1 2012.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!