MediaWiki-extensions-CommunityConfiguration works on top of configuration providers, which are defined by client extensions of CommunityConfiguration or in LocalSettings.php. When multiple extensions (or an extension and LocalSettings.php) define two providers on the same key, one of them is selected (LocalSettings.php has precedence, and ExtensionProcessor handles inter-extension conflicts) and at the end, used.
In this task, we should consider whether that behaviour is the expected one, and if we decide on a better approach, log a task for fixing it.