We noticed that there's a bit of confusion with the Dolby Surround settings, hopefully this will clarify some of your questions
There is no confusion regarding either how the Surround Sound settings worked before or how they work after the release of the tvOS 9.1 update. The only question is why Apple developers decide to first create and then leave a gaping hole in Dolby audio support on the TV4. By electing to decode "non-multichannel" Dolby audio within the TV4 device and pass it to downstream devices as PCM, Apple has, in effect, chosen to terminate direct, automatic "full" support of Dolby center channel mono, 3-channel Front, and active Dolby ProLogic II encoded audio content. When passed through to the AVR, such content was previously decoded and processed both automatically and correctly by AVR Dolby processing circuitry without further action on my part. However, following the tvOS v9.1 update, I must now manually ensure additional passive processor options are engaged to restore center channel (mono or 3-channel Front) and/or recover DDPLII surround channel audio for speaker output. Unfortunately, the application of these passive settings are themselves tied to "effect" options which now must also be selected and which further "colorize" and modify audio playback... And do you even want to go into the Dolby to PCM normalization and automatic loudness control issues experienced by some users when the Dolby encoding are decoded by the TV4 for PCM output?
The obvious remedy (or at least what seems obvious to many users) would be to add a fourth Surround Sound user option (Dolby Passthrough) to the current Auto, Dolby Surround, and Stereo TV4 option settings. This option would pass Dolby audio content (either AC-3 or E-AC-3) directly to the AVR for automatic decoding, post processing, normalization, and/or ALC handling as might be required. This is not anything new since AC-3 audio was "fully" supported in this manner prior to the release of tvOS v9.1 and the Infuse Pro app currently supports HDMI DTS passthrough on the TV4 at this time. In short, I don't know (or really care) why Apple developers insist on having a "Dolby Surround" mode option that cannot handle Dolby audio content not encoded with an LFE channel, but I am anxious for them to restore a "passthrough" option that does "fully" support Dolby audio as Dolby audio content.