I've been experimenting around with my setup. I have a Q80A 55" TV, Q990B soundbar and Apple TV 4K.
I've noticed that when the ATV4K is connected to the TV, and the digital output of the TV is set to Auto, Dolby Atmos will get to the soundbar, Dolby Atmos message appears on the screen of the soundbar, but the sound effects aren't all there. Digital output needs to ne set to Passthrough. The difference is very noticeable when listening to Atmos tracks on Apple Music, quite a different experience. I don't know what is the Auto setting doing to the sound other then sending it to the soundbar.
The thing is, when watching TV channels or the TV's native apps, we cannot select Passthrough, since the audio is not coming from a HDMI device, we're forced to use Auto. And the experience will be the same as using a HDMI device with the Auto option. I compared Netflix, Atmos works, but you don't have the same experience.
If we were able to select Passthrough when watching native content, it would solved this problem. Many people that don't have an external device to compare will probably never know that they're getting capped Atmos.
