We added our own checkstyle as a fragment, but we didn't find a way to select it as the default one (outside the UI).
Our usecase is for all newly created project, we'd like to have our corporate checkstyle selected by default (even in a new workspace:-)
You're right, it is currently not supported to mark built-in configurations as out-of-the-box-default.
I know it's a tad late but defining a builtin config as the default to use will be supported with the next version.
Changes are in branch https://sourceforge.net/p/eclipse-cs/git/ci/127_default_builtin_config/tree/
With this you can set a default-weight attribute in the plugin.xml defining the built-in configuration. Highest weight wins.