I also had a Gen 2 ATV4K swapped for a new unit, and it didn't help the Atmos problem. I also found tvOS 15.2 and 15.3 were far worse than 14.7, which was originally on the replacement. However, I also have a Gen 1 unit that has worked perfectly for several years under the same conditions, presumably running the same software. So it isn't that simple.
This is just a WAG, but I believe there is something different about the 2nd gen hardware that tvOS did not take into account or was not optimized for. My hypothesis is that the Gen 2 Atmos problem is due to errors in the creation and/or timing of the MAT 2.0 Atmos signal. Some folks with Gen 2 units appear to have no Atmos issues, while others have varying degrees of symptoms. I believe this is because some AVRs and Atmos decoders are more effective at correcting and/or masking the MAT 2.0 errors.
DragonByte79 just got an HDfury VRROOM, and so far his Atmos problems appear to be gone. This device acts like an eARC device, but extracts the HDMI audio from the HDMI signal. I believe it also provides error correction, so this would tend to support my hypothesis regarding the MAT 2.0 errors. I don’t believe there is any issue with the Gen 2 audio stream decoding or generation of LPCM output, as I would expect that to also affect other audio formats, since the ATV4K still decodes the audio and outputs LPCM, just without the MAT 2.0 Atmos container.
Again, this is all just a WAG.