I'm actually back to using the 2020 Ultra since I have this issue fixed. I stripped the header from all of my non BT2020 movies and the saturation problem has gone away. I like the fact I can decode basically all high end audio. Like DTS 7, etc.
So I think this might be an issue with my TV or Receiver. I have a Roku Express 4k+ in the basement with an Onkyo TX-SR333 and Samsung UN55J6200. I figured I'd just try the same movie there and see what happens. Well, surprise surprise, it worked 100% and direct played the HEVC and EAC3 audio, no issues, no color saturation, just perfect.
The setup I had been trying is Roku Express 4k+ with an Onkyo TX-NR646 and Sharp LC-60LE650. On this set up AC3 and EAC3 audio isn't direct playing.
Well, I figured it out. Not sure if it's a Roku issue, a Plex issue, or both.
Turns out the Roku in the den had its "Listening Mode" set to "Leveling." In this mode, AC3 and EAC3 audio was not being transmitted to the Onkyo receiver properly. I have yet to understand what the Roku is doing exactly that somehow is screwing with the audio stream.
When I turned the Listening Mode to "Off" the audio stream transmitted to the Onkyo properly and played back perfectly. Perfect direct play of both video and audio.
I really don't understand what the Listening Mode is supposed to do, but it is not handling AC3 and EAC3 properly. Maybe it's only able to handle AAC stereo? Regardless this seems like a pretty big bug and I'm glad I stumbled on this solution since it's completely not intuitive at all.
This "Volume Mode" setting is definitely screwy. When my kids next went into Plex to play a different video file there was no sound at all. Had to change the Volume Mode to Leveling, and that got the audio to play. Then tried all the other modes and they all worked (even the original setting, which was "Off"). There's some initialization problem with this setting that can only be fixed by changing the setting.
You have the color saturation issue? If so, having AAC surround sound is likely going to make it impossible to fix with just MKVToolNix, if my understanding is correct. From what I read here, Roku doesn't handle AAC surround sound properly, so Plex will refuse to send it that audio stream and will instead transcode the audio to AAC stereo. When it does that it has to repackage the video and audio streams into a new MKV container. This MKV container has a header with color info that Roku doesn't interpret correctly and you end up with color saturation (the colors are all shifted to red).
You can try fixing this in MKVToolNix without re-encoding the audio as AC3 or E-AC3. To do that, open the file in MKVToolNix under "Header Editor." You then want to strip away the "bad" header information found under "Video Track 1-->Colour Information." I'm not 100% sure which ones should definitely have the information cleared out, but it won't hurt if you just clear them all. Someone else earlier in the thread though it was "Video: Colour Matrix Coefficients," "Video: Colour Range," "Video: Transfer Characteristics," "Video: Color Primaries." My test video has zero header information under "Video Track 1-->Colour Information" so I don't think you can go wrong just removing whatever header information you see.