There's no need to set your AVR to pure direct. I have my Marantz set to Dolby Surround. The Stereo Upmix is disabled on the Shield.Why pure direct and not Atmos? Does that disable audessy?
I still get Atmos via Plex, Kodi/MrMC, Amazon Prime, and Vudu on my 2015 Shield.
The Xbox One uses Dolby MAT which means Atmos is engaged all the time, but when you check out what's going on in your AVR's web interface, Not everything is in Dolby Atmos. The Apple TV4K also uses Dolby MAT, but the output information is correct.