I am also having the same issue. It only started happening with the latest version of Apple tvOS which updated today.
I am having other audio issues - sometimes AppleTV is not detecting ATMOS availability I have to do a HotPlug to fix that issue and volume levels seem to go up an down on Netflix "Our Planet" a great test video.
Broadband Rate 52Mbps, 8K HDMI 2.1 Cables, 18Gbps 5 Port Gofanco Switch, Connected to HDMI 1 of Samsung 2020 UN50TU7000 and HW-Q70T Soundbar connected as ARC to the HDMI 2 of TV.
I have restarted the Apple Several Times.
I updated to the most recent (09/29/20 release) build 18K5036d and I had stuttering
Atmos or not, in YouTube, YouTubeTV and NetFlix. Disney+ with like Star Wars Episode IX - zero stuttering. Very strange.
**** edit, I do not even know what happened, but it fixed itself, maybe... this was a strange one, even for me. Netflix is fine, YouTube is fine, YouTubeTV fine, everything works now.
I reset TV, AppleTV, Sound Bar, still stuttering on those 3 apps but not in Disney+ in Dolby Vision and Atmos.
I changed TV output settings, eArc on and off, still stuttering. Force closing app, reopen, still stuttering.
Changing sound output from Passthrough, to Auto, from PCM to Bitstream. Still stuttering.
Changed all sound outputs to eArc, Auto. I've been on Passthrough since I bought this TV / soundbar setup.
So with everything sound to Auto. Force Closed YouTube, reopened and the video I had playing is no longer stuttering. YouTubeTV no longer stuttering. No audio stutters at all.
I am not sure if anything I did, fixed it, but I am a little hesitant to change settings back to potentially reintroduce a stutter because that was quite a frustration. No video stutters at all but audio stuttered every one second, it was just coming on, going off, coming on, going off, over and over.
The TV shows Dolby Vision when video changes, the only way I can sort of verify Atmos is enabled is the sound bar display will show ATMOS. And it
was stuttering in Netflix show with or without atmos, youtube no atmos or 4K 'yet', youtube tv no atmos but Disney+ never waivered a bit.
I am going to update the other, very similar setup in the bedroom and see if any audio issues show up and if any changes... changes anything.
Also just saw your comment on Atmos not being reported properly, neither of my TV's were reporting Atmos properly either with the previous AppleTV developerbuild, was showing just PCM, now showing everytime Atmos content plays.
LR setup : LG CX 77" OLED + LG SN11RG soundbar + AppleTV 4K, CableMatters '8K' 48 Gbps cables.
- AppleTV connected to TV, Soundbar connected through eArc
BR setup : LG C9 65" OLED + LG SN9YG soundbar + AppleTV 4K, CableMatters '8K' 48 Gbps cables.
- AppleTV connected to TV, Soundbar connected through eArc