On the General Volume & Audio Output settings page of the Xbox do you have the Allow Passthrough checkbox selected? In one pic you do and in the other you have it deselected. I think this needs to be checked for streaming apps to output audio directly to be decoded by the Amp.
I think the guidance is adding 3db to the level as assigned to the dolby speakers by Audyssey.
I have no experience of the XBox, but I wonder if the Allow Passthrough option should be ticked, to allow the AVR to decode the sound format?
THe XBox uses Dolby MAT to enable it to output Atmos. THe console decodes the DD+ or TrueHD element itself and then outputs this as multichannel PCM along with the associated Atmos metadata. THis differs to how you output it ordinarilly if using most other sources. Certain configurations need to be applied and you may be required to download additional software and or updates in order to fascilitate Atmos via your XBox?
No idea as to how to configure the XBox ONe or later models in order to get Atmos. You need to go ask this in a thread dealing with the XBox.