I am confused :o,
Do you mean that the output file did contain Atmos audio info, however, through your receiver, that Atmos audio track was transferred into Dolby Digital during playback?
Other movies that with the Atmos audio, can playback well on your receiver?
Also
1. What player did you use for playback? Did you try to adjust the audio settings?
2. More info is needed for your receiver.
3. Which profile did you use for the conversion? Please provide dvdfab_internal and fabcheck_internal log file for the process.
4. Please attach a copy of the mediainfo of the John Wick 3 output file.