This has to do with the way the harmony output is fed to the internal pre-amp. We experimented with different sytems, one of which was, as you suggested, including the harmony output with the mic output. In practice this made it difficult for users to easily control the balance between the harmony parts and the clean mic volume. Many users expressed the importance of being able to easily alter this relationship for different songs.
With the mic volume controlling only the direct output of the microphone, as it does now, you can easily change the relationship between the harmony and the live voice without having to go into any other menus. This, by popular vote, was agreed to be the most effective use of the MIC slider.
Chris