[eluser]Pascal Kriete[/eluser]
You need to work out what functions are being overriden and what effect it has. Then change them so that all desired effects are included.
Core library extensions are instantiated along with the base library, because a lot of the core library functions run before a controller is called. That means that CI has no reference to the current state of the application. That's also why dynamically calling them wouldn't work - it's too late by that point.
If you have a mutually exclusive conflict, you'll need to decide what behavior is more desirable.