Apple TV 4K -> EAC3 not sending atmos

Yes.

Unfortunately, Plex does not indicate when an audio track has Atmos. It only shows EAC3 or TrueHD.

You can examine the files using MediaInfo.

For EAC3 + Atmos you will see something like:

Audio
ID                             : 2
Format                         : E-AC-3 JOC
Format/Info                    : Enhanced AC-3 with Joint Object Coding
Commercial name                : Dolby Digital Plus with Dolby Atmos
Codec ID                       : ec-3

Understand.

AC3, EAC3, and EAC3 + Atmos should direct play and be passed to your Denon receiver.

However, as you’ve seen, subtitles come into play and can cause an audio or video transcode. When the audio is transcoded, any Atmos information is lost.

The part I cannot tell you is how subtitles affect things, as I’ve no way to test that myself.

Hopefully somebody with an ATV4K can chime in with additional information.