In order for a ConfigEntity to handle CRUD in the import process, each module must implement a hook for each operation, and then pass the config on to the entity system for saving. If this doesn't happen, the config system simply spits the config out to the target file system. It would be nice if, during the import process, we had a way to know whether a specific piece of configuration was static or handled by a ConfigEntity, and call the appropriate functions. We would still have the hooks for more elaborate needs, but we wouldn't force every module that implements a ConfigEntity to have the same boilerplate code that does nothing but call entity_save().
I will write a better summary later when its not 1:00 am and I haven't been up for 16 hours.