Since upgrading to Hibernate 5, Confluence can make Hibernate specify during schema creation that created tables should use InnoDB as their storage engine, no matter what the default storage engine of the MySQL has been configured to be. When this works, all CREATE TABLE DDL will have ENGINE=InnoDB appended. This will reduce setup and configuration pain when using MySQL.

Note that Confluence must upgrade to Hibernate 5.2.9 or higher in order for this technique to work. Note also that if Confluence changes its mysql default Dialect to org.hibernate.dialect.MySQL55Dialect or a subclass, then Hibernate will default to specifying InnoDB automatically.