No. Let it decode the signal and output LPCM. 2.0 and 5.1 tracks will be output to the corresponding channels without issue. A benefit of this is that the Dolby offset will not be activated at the receiving end.
With Change Format(Dolby Digital) OFF and the Immersive Audio(Dolby Atmos) setting ON, Dolby Atmos tracks will display as Dolby Atmos, not Atmos/DD+ because it is not a bitstream and has been decoded and converted to LPCM before being sent to the receiver. Other receivers will display the signal as Atmos/PCM when using a device that supports Dolby MAT.
There is no need to change audio settings for different audio signals. And, again, different apps and streaming services tiers may or may not support Dolby Vision and Dolby Atmos. The Hulu app does not support Dolby Atmos at all. It supports 2.0 and 5.1
Assuming all service tiers and apps used here support Dolby Atmos, except Hulu, the red Dolby audio indicator on the Onkyo front panel display should light up only when playing Dolby Atmos tracks using the Apple TV 4K with optimal settings. It should display PCM in green for all non Atmos signals.
Now, use the Smart TV’s apps and send audio to the receiver over eARC and things change a bit as the TV can bitstream signals. So, using the TV’s Hulu app, a 5.1 signal may display as DD+ 5.1 rather than MULTI CH PCM 5.1 when using the Apple TV 4K. Dolby Atmos bitstreams from the TV should display as Atmos/DD+ on the Onkyo. Atmos metadata from bitstreams can be lost and the streamed signal displayed as just DD+ if a non compliant speaker configuration is in play.
The Apple TV 4K does not support DTS at all. It cannot accept, decode or output DTS signals. The Sony TV here does support DTS and I believe is one of the supported models of Disney+’s IMAX Enhanced Signature Sound by DTS. If using the TV’s Disney+ app with highest service tier and selecting an IMAX Enhanced title, with a few exceptions, the IMAX DTS:X track should be an option for output. When using the Apple TV 4K, DTS:X is not available at all and Dolby Atmos will be output.