I think there is a reasonable use case for applying the default config: in my case, embedding IPython and the QtConsole basically gives me a way to interact with the application for parts for which I have written the backend but not yet the GUI frontend -- it serves as a "debugging" widget more than anything else.  Thus, I don't want to bother with another configuration (e.g. to make `%edit` work) when I am already used to my default configuration.

On the other hand I certainly don't claim that this is the proper way to apply the config so hints on how to do it properly are certainly welcome.