I don't know if everyone's seen this, but there's an interesting article on the Dolby Developer page that sheds some light on this.
Unfortunately, seems to be a "feature", not a bug. It states that:
Apple TV includes a built-in decoder for Dolby Digital Plus and Dolby Digital audio. This means that the Apple TV is able to decode Dolby audio rather than simply pass the compressed bitstream to another device
Decoding the audio inside of the Apple TV enables Apple to support several features such as mixing of other sounds from the system, Siri® voice input, and so on.
And goes further to explain that while the Auto setting will always send PCM audio (stereo, 5.1, or 7.1) to the connected receiver, the Dolby Surround setting is only intended to force the ATV to export a Dolby Digital compressed bitstream for older devices that don't support multichannel PCM.
When this [Dolby Surround] setting is selected, the audio is first decoded (although constrained to 5.1 channels) and mixed with other system sounds, and is then reencoded to the legacy Dolby Digital format just prior to the HDMI output. The connected device (TV, sound bar or AVR) will then receive a Dolby Digital bitstream.
Hence the issue we're all having. Unlike the ATV3, which would simply pass through the existing bitstream for the receiver to decode, the ATV4 is decoding everything, mixing with system sounds (and, per many of us, adding unwanted compression and dynamic range limiting), then RE-encoding it before outputting as a bitstream. It may or may not be factoring the Dialog Normalization into the initial decoding, but the re-encoding certainly sounds quieter and missing dynamic range compared to the original.
So basically, we are stuck with this arguably inferior AC3 bitstream because ATV4 insists on having a way to mix in system sounds. Until Apple decides to offer up a fourth sound option- passthrough- it appears this is the way this is going to stay.
I would suggest in any future messages to Apple, you mention that you as a user would like to see the option to passthrough the existing bitstream restored, even though we're aware that may limit Siri and other functionality that depends on mixing in system sounds (something I don't think anyone wants during movies anyway). Otherwise, it looks like this isn't a simple "oops we forgot to include that", it's another example of Apple saying "we know this is how we've always done it but we do it this way now, get on the bus."