This may be what you're seeing...
Blu-ray will show Atmos on your receiver if your Xbox is set to bitstream from disk. This is a specific setting for disc playback which it appears you have correct.
Outside of disks, in the general sound output settings you will have a number of options including Atmos, Dolby Digital, PCM, etc... The only way to get Atmos from games (and Netflix) is to change this setting to Atmos.
The problem this creates, which may not be a problem for everyone, is that Xbox will now output all your Atmos channels all the time. This means that a 5.1 channel source (in Netflix for example) will have the 5.1 channels but the other (Atmos) channels will be empty. This means your receiver can't perform any simulated Atmos processing on these sources (because it is receiving all the channels already, although some are empty).
The solution, though not elegant or convenient, is to set the Xbox output to Atmos when you're going to play a game (or Netflix show) with Atmos... then back to your setting of choice at all other times. This way you get Atmos when available, but when it's not your receiver can apply the processing of your choice to the available channels to utilize your speakers.
Leave your disk playback settings as-is.
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