Apple TV 4th Dolby Digital ??!

Why is this not automatic if I leave the Apple TV Audio Surround to Automatic as it should be?

Most likely, it is due to one or more TV4 programming changes.

1. First off, there is the question of the "channelization" and the tvOS version under which you are operating. In the TV4 "Auto" mode under tvOS v9.0, source track audio channels were output as corresponding channels of a DD+7.1 bitstream connection with receivers, amplifiers, or HDTV devices. This meant a 1.0 mono source track was carried as the "active" center channel of the DD+7.1 connection along with 7 "empty" channels; 2.0, stereo, and DD ProLogic II source content was actively carried on the Left and Right channels of the DD+7.1 bitstream connection along with six "empty" channels; DD5.1 sourced audio was "impressed" on corresponding L, C, R, SL, SR, and LFE channels along with "empty" RL and RR channels; and DD+7.1 supposedly being "passed through" to the target device. Unfortunately, many users were confused by this use of DD+7.1 bitstream connection to carry the various forms of source data (such as iTunes stereo music files) which automatically triggers the Dolby Digital decoder and complained to Apple regarding the matter. As a result, Apple issued the tvOS v9.0.1 update. This update "fixes" the problem by unconditionally sending 1.0, 2.0, stereo, and DD PL II content as L and R PCM channels. While this prevents DD+7.1 output confusion and disables any undesired triggering of the Dolby Digital decoder, it also disables "automatic" 1.0 center channel playback on my system.
2. Unlike older TV devices, the TV4 automatically selects the first "enabled" track for playback. This means that if your videos are encoded with both enabled AAC and disabled AC3 audio tracks, the AAC track is now automatically selected for TV4 output and you must manually select the AC3 track if you want DD Digital encoded data to be used as the playback source audio track. This, combined with the issue discussed in paragraph 1 above, may well be the answer your question. That is, if a 1.0 or 2.0 source audio track is being selected automatically and your are operating in the TV4 "Auto" mode under tvOS v9.0.1, then the TV4 is processing your sourced audio track as if your device were operating in the "Stereo" output mode which, as explained above, outputs the 1.0/2.0 audio as a Direct Stereo PCM connection which, of course, won't automatically trigger Dolby Digital decoding.
3. On the other hand, the TV4 "Dolby Surround" output setting still works using the tvOS v9.0 "Auto" strategy—only employing a DD5.1 bitstream connection in place of the "Auto" DD+7.1 bitstream connection strategy. If your videos are limited to 1.0, 2.0, stereo, DD PL II, and 6-channel content, then most TV4 users would likely prefer the "Dolby Surround" output mode. In this case, 1.0, 2.0, stereo, and DD ProLogic II AAC (i.e., non-AC3) source audio tracks are output as "active" channels "impressed" on a DD5.1 bitstream connection while AC3 audio track data is passed through in its encoded format to the receiving device for decoding and playback which, unlike non-AC3 sourced audio data bitstream connections, the receiving device accurately displays as correct channelization of the AC3 track as originally encoded. I.e., a 1.0 AC3 audio track decodes/displays as a mono center channel encode; 2.0, stereo, and DD PL II AC3 audio is decoded/displayed as DD2.0 content by the receiver; and an AC3 5.1 track is decoded/displayed as DD5.1 content while non-AC3 source data is always decoded and displayed as DD5.1 content no mater how many channels are "active" on the sourced audio track. (This can be confirmed by simply listening to each speaker's output individually.)

For me, the "Dolby Surround" option is the best output option since my library videos are encoded with primary AAC 1.0, 2.0, stereo, and DD PL II audio tracks and secondary AC3 1.0, 2.0, stereo, DD PL II, and DD5.1 tracks—i.e., I have no DD+7.1 content in my library and only access 7.1 multichannel audio sourced from optical BD which by-passes use of the TV4 until such time as a 7.1 encoding workflow becomes available for my iTunes managed library. This mode currently provides correct speaker playback of all of my files despite AVR "display" inaccuracies and the need to manually activate DD PL II post processing since my AVR does not automatically apply such enhanced post processing in the "Auto Surround" mode alone. (I.e., my goal is correct playback "substance" over "form" while others may prefer a "form over substance" workflow so there is no "correct" setting for everyone.)

For a not expert person like me, the easy and practical question is: with all the new Apple Store Movies standard and ATV4,

-by setting Audio Surround to Automatic, my HT is showing Dolby Pro Logic II (on top of other modes like Theatre Dimension, T-D, etc);

-by setting Audio Surround to Solby Surround, my HT is Showing Dolby Digital.

In both cases, the quality and the experience that I am having is quite similar.

What would you do in this situation?

As previously indicated, this is primarily a matter of personal preference. In my case, I know how my audio tracks were encoded—with both AAC and AC3 audio tracks—and I normally prefer to play the AC3 track so that my receiver correctly identifies/differentiates/plays 1.0, 2.0, and 5.1 audio content automatically. In your case, it will probably be impossible to tell how your movie purchases were encoded except by examining source files on your computer or by listening to individual speaker playback. My best advice would be for you to play some "test" files in both the "Auto" and "Dolby Surround" modes in order to examine various output "idiosyncrasies" depending on the source track compression format, TV4 mode, and encode channelization. If you don't have a selection of such files available, here are a few you can download and test:

http://downloads.walker4.me/Temporary_files/Test-1.m4v

This video clip has both AAC mono and AC3 mono audio tracks. It is coded to open automatically with the AC3 track pre-selected. In the TV4 "Auto" mode both tracks should normally play as L/R 2-channel audio with DD PL II disabled or center channel mono with DD PL II enabled. In both cases your AVR should identify the audio as Stereo PCM under the tvOS v9.0.1 update. In the "Dolby Surround" mode the AAC track should also play as L/R 2-channel audio and be unable to decode the mono center channel since your AVR should identify the bitstream as being DD5.1 multichannel connection. However, the AC3 track should play back automatically as the original mono center channel track and correctly identify the DD1.0 bitstream as such.

http://downloads.walker4.me/Temporary_files/Test-2.m4v

This video clip contains AAC 2.0 and AC3 2.0 audio tracks. Both are encoded for DD PL II playback. Once again, in the "Auto" mode both tracks with play as L/R Stereo with DD PL II enhancement disabled or with added center and surround channels with DD PL II enabled. Again, your AVR should identify the input audio as Stereo PCM in this mode. In the "Dolby Surround" mode, however, the AAC track will again be identified as being received as a DD5.1 bitstream with only the L and R channels active and DD PL II decoding disabled. On the other hand, the AC3 track should be identified by your AVR as Dolby 2.0 audio which can be played with or without DD PL II enhancements.

http://downloads.walker4.me/Temporary_files/Test-3.m4v

This last video clip is encoded with an AAC 2.0 DD PL II track and an AC3 5.1 audio track. In the "Auto" mode, the AAC track with be identified as Stereo PCM and, like the file above, can be played back in stereo with or without DD PL II processing. However, the DD5.1 AC3 track will be identified as a DD+7.1 audio track which only plays with 6 active channels. In the "Dolby Surround" mode, the AAC track again plays as stereo with or without DD PL II enhancement but is identified as a DD5.1 bitstream. The AC3 track is also identified as a DD5.1 bitstream but, in this case, all 6 identified channels are active.

As you can see, there is give and take no matter which way you go. So you may as well pick the workflow that suits you best personally—as long as you the associated weaknesses.

Let's hope this mess is fixed in tvOS 9.1, which is at the beta3 stage right now. In my opinion, the state it is in right now, it has no business being part of either home entertainment setups that I have. One of which is a simple 5.1 54" sound bar setup and even it is smart enough to realize there is something wrong. Again, this is just my opinion.