I agree with johan rebel the Waterberg Plateau makes a great stop over between Etosha and Windhoek. From there you are a 3 and a half hour drive to the airport + some extra time for filling up the rental vehicle, and maybe a quick stop at Okahandja to buy some last minute presents - so leaving from the Waterberg around 08h00 should give you plenty of time (always add in a buffer - and stop in Windhoek for lunch if the journey goes smoothly). Fortunately it is tar road nearly all the way. The Waterberg is scenicall a very beautiful area and the trees will be a great contrast to the almost bleakness of Etosha at the time (and that is not meant to be negative, Etosha in September is nothing short of awesome).
If you do head to Damaraland, it is stunningly beautiful, probably my favourite area of Namibia. It will just mean more driving, and a lot of your extra 2.5 days spent behind the wheel rather than relaxing (although through Damaraland often the journey is spectacular). Maybe think of staying at Camp Kipwe if you do go - great little property.