Fire TV stick or Apple TV or any other device (STV, Xbox) will only output what the Prime platform streams. Dont blame your device if Prime is at falut. Looks like Xbox alone is upscaling, I wouldn't call it Atmos but more of a DSP output.
If Prime streams Atmos in DD+ or THD variations (both are valid Atmos streams), I am sure Fire TV, ATV, STV etc will pickup the same. The problem lies with Prime platform rather than the devices.
Atmos audio stream may not show the atmos specific channels in the input (
reference), looks like only the atmos specific objects are added to the base 6/8 channels in the BD and OTT streams. I am yet to completely understand this.