Why mysql-noinstall5.6.x.zip includes ibdata file?
To give you an more extensive answer, inno_db stores these data
data dictionary aka metadata of InnoDB tables
change buffer
doublewrite buffer
undo logs

so there is a lot of information and it can get really big.
so mysql 5.6 stores there data, that it needs when it is restarted, and 5.5 doesn't.