If you like the sound you are getting now, that is all that matters. But, connecting the Apple TV 4K directly to the TV means you will not be able to superimpose the Yamahas menus over content from the Apple TV 4K as they are using separate inputs into the TV, if you haven't disconnected the Yamaha from the TV altogether.
The Apple TV 4K will output uncompressed PCM by default. The TV may be converting it for output of Dolby Digital 2.0/5.1 to the receiver. You can achieve similar results with the Apple TV 4K connected directly to the Yamaha. Go into the Video and Audio settings of the Apple TV 4K after connecting to the Yamaha again. In the audio settings, select Change Format to change the output from Best(uncompressed PCM) to Dolby Digital 5.1. This may give you the sound you are enjoying now using the optical output from the TV.
Some will cry foul at the thought of converting the signal. Remember that all Dolby signals are lossy and compressed when streamed from a service. This includes Dolby Digital Plus 7.1 based Atmos tracks. The Apple TV takes that signal and repackages it in a nice clean uncompressed PCM box and stamps an Atmos sign on it so the receiver can pick up the metadata. They call this process Dolby MAT. With only a 2.1 setup, the Yamaha would not pickup the Atmos metadata anyway. You need a 7.1 or a 5.1.2 configuration for the Yamaha to make use of metadata.
If you have not done so already , go into the Yamaha Amp Assign section and set it to basic. Then, go to Configuration and set the Surround, Surround Back and Presence speakers to NONE. With 2.1, you can just leave the Decoder at Straight or DSP mode to 2ch Stereo.