As the name suggest, MySQL has traditionally been all about using SQL statements to execute queries. This is not just reflected in the language used to describe what the queries should do, but also in the underlying way the data is structured. The MySQL Document Store turns this upside down and provides not only a NoSQL database, but also uses JSON documents, like other document stores use for storing data.
The Document Store does not replace the SQL database. The two are meant to live side by side, so you can use whichever works the best ...