Diagnosis
Your signal chain is not passing through a full Atmos audio signal. The most common cause is incorrect TV settings acting as a bottleneck.
How to Fix It
Bypass the TV. Connect the Apple TV directly to the soundbar's HDMI IN port.
1. Connect Apple TV 4K to the HDMI IN port on the Yamaha SR-B40A.
2. Connect the SR-B40A's HDMI OUT (TV ARC) to your TV's ARC/eARC port.
3. On the soundbar remote, select the 'HDMI 1' input.
4. On the Apple TV, go to Settings > Video and Audio > Audio Format and set it to 'Auto'.
5. Now play known Atmos content (like a movie on Apple TV+). The soundbar's display should cycle and then show 'Dolby Audio' for Atmos content.
If That Didn't Work
Your TV's internal audio settings are likely downgrading the signal. Even with eARC, some TVs need manual configuration. In your TV's sound settings, set 'Digital Sound Out' to 'Pass-Through' or 'Bitstream', and disable any internal sound processing like 'Audio Delay' or 'Smart Sound'.
Heads Up
The SR-B40A uses virtualized Atmos (Dolby Atmos Height Virtualization). It will never show 'Atmos' on the display, only 'Dolby Audio'. The 'Surround' indicator means it's receiving a standard 5.1 or 7.1 signal, not the object-based Atmos metadata.