While not understanding exactly what you have going on, I would concur that an interceptor afterConfurationLoad or afterAspectsLoad might be something to look into.
To answer your question about a CFC which lives outside of ColdBox, you could create an instance of a proxy object and have it retrieve whatever you need since it knows how to contact the ColdBox application. Of course, you can’t access CacheBox until the framework is loaded anyway which brings me back around to my (well, Andrew’s) first suggestion of creating an interceptor to listen to application startup and set whatever config you want right then. Interceptors have access to everything.
ColdBox Platform Evangelist
Ortus Solutions, Corp