It is up to the app on how it does it but all of this should still happen in the digital stage. Think about it, an application should not be able to mess with the iOS's amplifier.
My only guess is that these apps effect the audio stream in the digital stage before it hits the DAC of the E07K. Thus the newly transformed signal is processed through the DAC and amp of the E07K.
But of course, this is just a logical guess.