You could try adding a subclass of ERXFrameworkPrincipal to your model framework. It will get loaded even before the Application constructor so I think you could do all your model swizzeling there.
/**
* Principal class of the ERExtensions framework. This class
* will be loaded at runtime when the ERExtensions bundle is
* loaded (even before the Application constructor is called)
* This class has a boat-load of stuff in it that will hopefully
* be finding better homes in the future. This class serves as
* the initialization point of this framework, look in the static
* initializer to see all the stuff that is initially setup when
* this class is loaded. This class also has a boat load of
* string, array and EOF utilities as well as the factory methods
* for creating editing contexts with the default delegates set.
*/
public class ERXExtensions extends ERXFrameworkPrincipal {