[RockerC]

Is there any chance one could use Kodi on the Pi3 to stream the audio to the Chromecast audio instead of HDMI, while still streaming the video over HDMI ?

Not likely. Kodi is all open-source, and Chromecast is proprietary/closed software from Google.
Those two types do not mix will in ourview. Thus, Kodi has no support for Chromecast, for audio or video.

FYI, Chromecast is closed source but the Google Cast protocols have been reversed engineered and then that reverse-engineering effort that been released as open-source libraries, just as an example check out PyChromecast:

https://github.com/home-assistant-libs/pychromecast

PyChromecast is has been actively developed for over 5-years as a popular feature in the Google Cast integration for Home Assistant (it was even developed by its founder): 

https://www.home-assistant.io/integrations/cast/

PyChromecast is only one of a few reverse-engineered libraries for Google Cast protocols but it probably the most mature. stable, and best maintained:

https://pypi.org/project/PyChromecast/#history

Many if not most protocols that Kodi do supports today are or have at some point been proprietary/closed source but have been reversed engineered and then that effort has been released as independent open-source code libraires.