This is actually not the case for me.
Was referring to the changes in the manner by which the data is forwarded by the TV4 to the AVR under tvOS v9.0.1 and v9.1 updates. However, if you wish to compare automatic post-processing by different AVRs, then lets look at some differences between your Denon and my Pioneer.
The update has fixed the Dolby Surround mode issue on my Denon AVR-2311ci so that my receiver sees 2.0 channels and automatically decodes it into Dolby Pro Logic II just like my ATV3G does.
Unfortunately, my receiver is programmed differently than yours. My receiver is not programmed to automatically apply Dolby Digital ProLogic II post-processing to Stereo PCM (AAC 2.0 sourced); "multichannel" (DD5.1, DD+7.1, 5.1 PCM, or 7.1 PCM); or AC3 1.0, 2.0, or 2.1 audio content. It only applies automatic Dolby Digital ProLogic II post-processing to AC3 "active" DD PL II encoded audio. (I.e., this is an older, pre-Dolby ATMOS, pre-4K UHD 60p/4:4:4@18 Gbps throughput, pre-etc. receiver model which I have yet to update.) Therefore...
Under tvOS v9.0.1 and operating in the "Dolby Surround" mode, my AAC 1.0, 2.0, stereo, and DD PL II content was sent over a DD5.1 connection between the TV4 and my AVR with only the Left and Right 5.1 channels populated with audio. As you will note above, this did not activate any automatic post-processing or enhanced audio routines. Using the same TV4 and AVR settings with an AC3 sourced audio track sent the AC3 bitstream data in its original encoded form (1.0, 2.0, stereo, 2.1, active DD ProLogic II, or DD 5.1) to my receiver for decoding and playback. As a result, 1.0 audio played through the center channel speaker; 2.0 and stereo content played through the left and right front speakers; 2.1 tracks played through the left, right, and LFE speakers; active DD PL II played as 3.1 with or without "surround" speakers as originally encoded; and DD5.1 played normally through the 5 front and surround speakers along with LFE. Thus, I sat, fat, dumb,, and happy—not even aware that others were using receivers that automatically enhanced any or all 2-channel audio inputs. (I.e., my receiver makes me turn on such enhancement features manually if I want them used.)
Under tvOS v9.1 and operating in the same TV4 "Dolby Surround" mode, both AAC and AC3 1.0, 2.0, stereo, 2.1, and Dolby Digital ProLogic II content is pre-processed by a routine (probably the "Stereo" mode downmix routine) before being passed to my receiver as "Stereo" PCM (i.e., the same connection used by older TV devices for AAC sourced audio tracks). Thus, any 2-channel audio content (or "multichannel" content output in the "Stereo" mode) sourced by your TV4 should now trigger automatic audio enhancement if your receiver is so capable (as you have already stated) while the "pseudo-5.1" playback of your DD PL II audio under tvOS v9.0.1 would automatically disable automatic post-processing of "multichannel" content. I.e., use of a 5.1 multichannel" connection between the TV4 and your AVR (whether they carry 6 channels of audio or only two) to carry your 2-channel DD PL II audio under tvOS v9.0.1 tells your receiver that no automatic post-processing is required.
5.1 already worked correctly.
As previously noted, sourced AC3 5.1 is passed in its original bitstream form under both v9.0.1 and v9.1 allowing your receiver to handle the decoding and playback correctly on its own.
Auto for me has not changed for me. 2 Channel audio is sees as 7.1 channels by my receiver, but is correctly decoded into Pro Logic II. 5-Channel audio is seen as 7 Channel audio and reports as 7.1 Multi-Channel Audio.
I see a number of changes in the "Auto" mode. Under v9.0, and v9.0.1, audio data was sent over a 7.1 "pseudo-connection." I.e., the receiver always indicated a 7.1 connection but only carried "active" audio channels based on the sourced audio tracks. Under v9.0 the audio appears to have been "impressed" directly on the same channels as the sourcing content. E.g., an AAC 1.0 audio track was placed on the center channel of the 7.1 connection. However, under v9.0.1, the same AAC 1.0 audio is preprocessed and changed to 2.0 mono before being sent via a "Stereo" PCM connection. However, "multichannel" content always skips "Auto" mode pre-process under all three tvOS releases. However, under v9.0 and v9.0.1 my receiver always indicated a 7.1 PCM connection and never indicated any LFE processing. On the other hand, under the latest v9.1 release, DD5.1 sourced content now actually displays as a 5.1 PCM connection and correctly displays active LFE processing on my receiver. Unfortunately, all 1.0, 2.1, and Dolby Digital ProLogic II content is still pre-processed under v9.1 before being sent to my receiver as "Stereo" PCM the same as using the "Dolby Surround" mode so I still have my problems in either mode.
What kind of receiver do you have?
Am currently running an older Pioneer VSX-1120 but am considering the purchase of one of the Pioneer Elite VSX-90 series models. As I previously noted, its features are rapidly becoming outmoded and it may be time to upgrade soon.
Did you buy from Apple, or someone else?
I purchased units through both the Apple On-line Store and the local Apple Store near my home. (I.e., the local store was stocked three days before pre-order purchases were scheduled to be delivered—even paying for 1-Day delivery.)