Of course we are concentrating on the current release builds of OSX but I appreciate your feedback on the beta versions. Apple always seems to want to monkey with Core Audio and not document their changes. This was a major issue for us in Mavericks and never got resolved until Yosemite was released.
That being said we will run some more tests with Spotify and Netflix to be sure.
Regarding Sparkle; we will close the update window after the new installer is launched.