The configuration saves the list of applications not to display in the Applications Panel.
However, it's not the role of the Panel Application to decide which applications should be displayed or not.
Instead, it's the role of the flavor to do it.
In order to avoid some merge issue, the best thing is to not provide any configuration by default, but create it when the administrator set in the administration (lazy creation).
(Mail thread: http://markmail.org/message/wo5zzajubr7je2ly however latest emails are not archived due to some problems with markmail.)