Anyone figured this out yet? Bought the new remote today for use with my existing Apple TV 4K and ran into this same issue.
As far as I can tell, mute works fine over HDMI-CEC but not at all over IR. Despite the setup letting you record the mute command from an original remote, which I obviously have done of course…
Unfortunately the old HDMI version implemented on my 10 year old receiver supports neither 4K nor HDMI-ARC. So I have to connect the Apple TV directly to the TV and then an old school optical audio cable to the receiver, and control volume over IR.
One very weird thing is that the LED on the Apple TV itself flashes for each button press on the remote – except for the mute button. And this regardless of whether the remote is set to Auto (which defaults to HDMI-CEC) or recorded IR.
Apple TV has the latest non-beta firmware installed, as of today 14.7. Remote version is specified as 0x0061 which may or may not already include the update supposedly released yesterday. And again, I have recorded the IR command for mute.