How to Reclaim Data Free in InnoDB Tables?
Everything you have done is correct in order to drastically defragment innodb tablespaces (there are other ways, but exporting, deleting files and importing certainly works).

Trying to optimize the tables (which, by the way, the correct way to do it for innodb is running ALTER TABLE mytable ENGINE=InnoDB- OPTIMIZE table just calls this, and REPAIR table does nothing for InnoDB) just after an in-primary-key-order import is useless. The way InnoDB works is optimising for access and write performance, not for data size. You will always have overhead in disk space (even if free space says 0), as innodb reserves spaces in whole extend beyond a certain size. Also, some data types, like blobs and random inserts and deletions can lead to extra fragmentation, but I presume that the size you are showing is less than 10% of the table size, so you should no worry. After a proper import, it is the least fragmented way innodb can work with the default options. Under normal operation, the file size should be constant when inserting new data until no more free space is available.

Of course, you can try to change parameters like extent or page sizes, but if you are concerned about saving disk space over performance I would recommend you to try compression (InnoDB Barracuda file formant has it) or use a different engine. However, please note that fragmentation and having huge files with lots of free space is usually not a concern with innodb_file_per_table = 1 under normal loads.