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There's no way to change the default connection factory tuning. If you need to tune a CF setting for an app that's using a default CF, then tuning is accomplished using the steps you mentioned: (A) configuring a custom connection factory, and (B) changing apps that need specialized tuning to refer to the JNDI name of the custom connection factory.
It's often helpful to use "Foreign JMS" to enable changing an app's CF without changing the app. See http://docs.oracle.com/cd/E21764_01/web.1111/e13727/interop.htm#i1009775
WebLogic Messaging Development Team