Many forex broker use MetaQuotes Report server. It let them use all power of relation database engine to build complex reports with no load to MT4 at all. But sometimes it might be not enough.
Standalone application that extends data exported by MetaQuotes Report server with additional tables for symbols settings, quotes, jourmal records etc.
So you will be able to make SELECT with JOIN request to the MySQL DB by using all data that MT4 has.