Database schema size result differs from file size when exported
The export does not contain the indexes. It only contains the definition of the indexes but not the data that is stored in there.

Additionally the size of SQL export will also not reflect the size of your data (just think of the SQL keywords that are needed for the SQL export).

When you move data from one representation to another (MySQL "on-disk" format -> Binary Export -> SQL Script) it is to be expected that the different formats show a different size. 

But I don't understand what you problem actually is.