There should be a "Based on Source" option for the audio as well as video.
Many issues with the Premiere Pro Project Manager, Proxy Creation, and Ingest can be avoided if you could simply have presets that work with all audio configurations. In many instances you would want the transcoded media to have an identical audio layout to the original. Its essential, in fact, when creating proxies and archiving sequences using Project Manager....yet, there is no option to do this.
It's silly that a proxy file needs to match audio settings, but if Adobe really needs it to be so, then at least make it possible to match source audio!