Dolby atmos not showing on Apple TV 4k

The Apple TV should be connected directly to the AV receiver, not the TV. (Apple TV 4K uses a high bandwidth form of Dolby Atmos that doesn’t work over ARC connections.)

Apple TV → AV receiver → TV ✓ works with Atmos

Apple TV → TV → AV receiver does not work with Atmos

It will only show this option if it detects Dolby Atmos capability in your audio system, and if you have it connected as needed.

Play audio in Dolby Atmos or surround sound on your Apple TV - Apple Support

Please disclose your Dolby Atmos equipment.

Just because you have the equipment does not mean it is set up correctly. I am not saying yours is not, I am saying just don't assume that if the specifications says it does something that the system is automatically set for that functionality out of the box. Please ensure you have you Apple TV set and the Yamaha set correctly as well. Finally ensure all connections are very high quality including your networking.