I am having the same problem. The menus for shows like For All Mankind and Prehistoric Planet show Atmos, but my Yamaha receiver is only getting a Dolby Digital signal. The receiver display shows Atmos while I'm in the menu, then switches to DD the second the program starts. Atmos worked fine on those shows previously. All other apps like Netflix and Disney still outputting Atmos just fine.
I've uninstalled and reinstalled the app and that didn't fix it. To make it a bit more odd, a movie I rented via iTunes but watched on the Series X apple app DID play in Atmos. But when I tried both the shows above after that its still only DD.
My setup is a Series X passed through a Yamaha RXV581.
There are other people on here and Reddit reporting the problem.