It seems like the documentation gives a few hints on how to answer this question:
The first one is if you've installed JIRA and connected to Oracle in the past and have manual configuration or custom settings, then you should configure manually as stated here:
If you had previously specified any additional custom settings while manually configuring JIRA with Oracle below (for example, adding the <connection-properties>SetBigStringTryClob=true</connection-properties> element to your dbconfig.xml file), these custom settings will be deleted upon clicking the 'Save' button and you will need to reinstate them manually.
The other two reasons mentioned would also mean you would need to configure manually:
1. If you use the JIRA WAR distribution or
2. you have a console-only connection to your JIRA server.
Perhaps some other folks have some input, but based on the documentation I'd take a look at whether or not any of the above apply and also look at the docs on known issues with Oracle to see if any of those might require custom settings. If this is your first time installing JIRA and connecting to Oracle and you can use the GUI then I'd try that and perhaps apply custom settings afterwards if you need them. I'm guessing you'll need to customize the settings though, I seem to recall the connection-properties issue (SetBigStringTryClob=true) being a must. That's explained in the bottom of the link you provided:
If you start experiencing problems when dealing with custom workflows or working with issues that have long descriptions, comments or custom field values, try adding the element <connection-properties>SetBigStringTryClob=true</connection-properties> as a child of the </jdbc-datasource> element in your dbconfig.xml file. Adding this connection property may overcome these problems. Be aware that you will need to restart JIRA for this setting to take effect.
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