Yeah, I've tried the "keep audio device active" as well. I've literally tried any of the audio configurations available within expert mode and still got the same thing. This is quite specific to these Intel Chipsets and Realtek HD audio devices that are sometimes referred to as Azalia.
Oh, sorry, forgot the other half. If you leave the BIOS as-is you will never get any devices recognized by ALSA so within the BIOS setting Chipset>South Bridge>Audio Controller set it to "disabled" (I know, a bit counter intuitive).
After that Kodi will list the audio devices differently because they'll be recognized by ALSA and show up with the "ALSA-" prefix in their name. No more popping or static.
Also any places in the BIOS that reference "High Precision Timer" I have set disabled because HPET is not ideal for devices of this vintage that show video. Also generally disabled ACPI where I could. This system has a problem where it misses or repeats USB events and hpet was a contributor when I was running Ubuntu or Mint on it.
I didn't have to edit Autostart.sh to get great audio & video, but I'll keep track of it and leverage that if I need to. Thanks for the input Nicolas.