At the moment all my hardware (Shield Pro, TiVo 4k, etc.,) is hooked up to the yamaha receiver which in turn is connected to my HD projector...but the video format shouldn't affect the audio feed/codec... should it?! And as I mentioned, I can get Atmos in Netflix, but not the other apps I mentioned. (Thanks for the response BTW)
Trouble is, multiple things can affect what formats are used for audio and video. You've got settings that you choose for the devices. You've got handshaking between the devices for what they are capable of (and this may or may not override your chosen settings). If you are using apps on smart devices, they may or may not fully utilise whatever the devices are allowing.
And then you've got the content itself, and whatever is made available on different streams. For example, my satellite provider only makes Atmos soundtracks available on UltraHD broadcasts / downloads. It's entirely possible for a streaming app to select a stream based on video capabilities, and that have an impact on what audio format(s) they make available.
I have a similar issue on the video side with a Chromecast (/w GTV) - depending on how/when the handshaking takes place, sometimes apps don't detect that they can use Dolby Vision, unless I reboot the Chromecast.