While I haven't tested it my understanding is it would only be for games with 3D audio (Tempest audio or whatever) and games custom made for Atmos. If the console is still outputting Atmos for other games it may just be to keep the system from having to switch and drop audio for a second, but I assume no audio will come out of those channels.
Destiny 2 doesn't support 3D audio, yet I get the directional sound effect when playing it with Dolby Atmos enabled.
It even does it with games like Fall Guys, where if someone uses an emote you can hear what direction it's coming from. Not useful, but a good example of the Atmos feature working.
If you are using a TV with just stereo speakers that has nothing to do with Atmos, if you have surround sound 5.1 that's again not Atmos, you need height/ceiling channels for Atmos. It sounds like you are just appreciating good stereo audio.