From my testing and all the reading of this thread and several others on the topic, you should be getting the same if source is AC-3 (which is Dolby Digital 5.1 - to answer your Q. to bodosom) and ATV4 setting is auto or Dolby Surround.
I've been following and contributing to the threads (here and at avsforum) on this issue since the weekend of the release. I have a 7.1 setup and was looking forward to finally having 7.1 sound from my collection via ATV.
I'm not familiar with the 2 channel stereo issues because I have a separate 2-channel system not built for A/V (just A) and there is no ATV there.
This being said, I am still not sure if I actually have a problem since I think I haven't run across a verifiable E-AC-3(which is Dolby Digital Plus) 7.1 source that can feed through ATV4. I see via the tvOS that iTunes Terminator Genysis offers DD+7.1 but I cant bring myself to purchase (my opinion here) horrible movie for the sake of testing this. Someone somewhere said they successfully got a DD+7.1 experience after buying that movie through ATV4 (note that is important because on a Mac iTunes only shows a 5.1 version).
I am convinced there is some sort of problem here because at a minimum if I set ATV4 to Auto and send it a verifiable DD5.1 file, I don't thing my AVR should show PCM 7.1 (even though it sounds like a legit DD5.1 soundtrack using 6 speakers).
If anyone can get their hands on a DD7.1 test file in .mp4 format that might answer at least half the outstanding questions....