I'll use the Shield later today and report. I expect video to be the same, and audio to just work.
As expected, the NVidia Shield Pro had zero audio issues playing an episode of Drive To Survive.
I played half the episode via the AVR, and the other half on the pickier Smyth Realiser A16 Atmos headphone processor. Both displayed Atmos at all times, meaning that the audio format does not change, even when paused.
using the info screen on the A16 we see that the audio format is Dolby Digital+ With an Atmos mix
so the conclusion is that the root problem is the ATV 4K and the mechanisms it uses to generate the audio streams for the downstream processors. If it were to pass the bitstream unmolested, it would behave much like the shield.