Yes! That was included with SQLyog version 5.1. The SCHEMA SYNC tool now syncs all available information from the database schemas and can be used across all MySQL versions with these exceptions:
1) it does not 'strip out' partition information when syncing MySQL 5.1 partitioned tables to MySQL 5.0 (it does when syncing to versions before that).
2) MySQL TABLESPACES (introduced in MySQL 5.1 for NDB tables and in 6.0 for FALCON tables) are not sync'ed. This limitation applies to the TABLESPACE itself as well as TABLESPACE usage in CREATE TABLE statements
Note that charset/collation 'defaults' for databases, and tables are synced from version 6.0 and charset/collation information for individual columns is sync'ed from version 6.1. Support for EVENTS was added in version 6.5
Note that to use the SQLyog/SJA data sync -functionality the order-of-tables must be identical. The structure sync tool as of SQLyog 5.1 will make that easy for you! However you can also use the 'reorder columns' functionality of the TABLE -menu or -pop-up-menu.
Also read this note on case-sensivity