On each documentation page that instructs how to configure Jira to connect to a database (like Connecting JIRA applications to MySQL) there is a full list of steps to achieve a successful connection, and at the end there is a list of known issues.

The suggestion is: given that from the 4 supported databases, only 2 have a Known Issues section at the end, and that MySQL particularly has several shortcomings, it might be a good idea to highlight the known issues right at the beginning of the page, either with a warning or message indicating this, as the way to solve some of those issues is to ultimately switch to another database (like the 4-byte character issue). For comparison, here are the links to the documentation of each supported database as of Jira 7.8:

• Connecting JIRA applications to MySQL
• Connecting JIRA applications to PostgreSQL
• Connecting JIRA applications to SQL Server 2012
• Connecting JIRA applications to Oracle