The current settings system is quite complex and has some limitations:

• impossible to reset a configuration array
• very complex (and sometimes impossible) to integrate configuration from a bundle in the siteaccess configuration

This is mainly due to the order of operations done to handle the configuration. Basically, the siteaccesses configuration are built while processing the configuration of the EzPublishCoreBundle, so any configuration outside of it can not be easily integrated in the siteaccess configuration because when the code from a bundle is triggered to handle its own configuration, it has only access to the end result of the settings merge and thus it's impossible to know if a given setting should be overriden by the bundle or not.