Provide a way for a parent app (or a parent module) to override a module's settings that it is dependent on. If we start thinking of modules as stand-alone libraries that can be uninstalled or reinstalled at any time we don't want to have to modify the core code of someone elses module after we install it to change the settings I want.
I'm thinking something similar to jQuery where a library will usually have a DEFAULTS object you can override, but you're never expected to install a jQuery plugin and then modify the core code to add your settings.
Give apps and parent modules a "modules" struct in their settings like how it's stored now, but you could actually declare it in the config. The actual modules settings will be appended to this existing struct.
/config/ColdBox.cfc or /modules/parentModule/ModuleConfig.cfc