You didn’t mention the MAT 2.0 stream that accompanies the LPCM 5.1 stream and carries the Atmos metadata. Months ago, I posted my thoughts that this is where the problem is. I believe the ATV4K Gen 2 is introducing timing issues or other errors in the MAT 2.0 stream. I believe the Atmos decoding is fine, since other audio formats have no issues. I have found certain programs, such as Drive to Survive on Netflix, to be more problematic. I believe this is because the video has more bandwidth and perhaps a busier Atmos track.
HDMI cable quality made no sense to me, since it seemed absurd that it could target Atmos only and leave all other audio formats and more susceptible video completely free of artifacts. I initially considered a thermal problem, but quickly ruled that out when I had dropouts within a minute or two of plugging in my ATV4K. My Gen 1 unit has been flawless in the same setup. And yes, a bitstream option would obviously solve the Atmos problem, and this has often been suggested here and in other threads.
I get a chuckle at posts that say the problem is 100% software. It isn’t that simple. For example, there could be a subtle hardware change that was overlooked in the software. For example, the software could have a bit of asynchronous code that expects the hardware to run at a certain speed. With the faster Gen 2 hardware, this could cause a timing issue. This could possibly explain why the Gen 1 and Gen 2 ATV4K do not behave identically with respect to the Atmos issue, assuming the same software. However, I do believe that the problem can be fixed or mitigated through software, since the Atmos problem was an order of magnitude less frequent on tvOS 14x.
Apple has been a major disappointment. If they aren’t going to fix the problem, either due to lack of effort or talent, they should give us a refund. We should not have to put up with these Atmos problems.