You may need to alter the audio output settings in Apple TV 4. I think they are not helpfully labelled. My Apple TV 4 was playing Netflix content in PCM multichannel (i.e. decoding the Dolby Digital audio to multichannel PCM) by default, and only when I changed the audio setting did I get a Dolby Digital bitstream to my Amp over HDMI instead. It may be your Apple TV is defaulting to PCM 2.0 output rather than bitstreaming because it doesn't think your TV can handle multichannel PCM (or Dolby?)
On my system, the global "Surround Sound" setting determines the audio format output by the unit irregardless of the audio format encoded in the source file. In the "Auto" mode, the TV4 outputs audio in PCM with the source track mapped to 7.1 channelization—i.e., my enabled DD ProLogic 2 AAC stereo track is output as PCM stereo mapped to 7.1 stereo channelization and my secondary disabled DD5.1 AC3 surround audio track is output as PCM surround audio mapped to 6 of the 7.1 channels as programmed. On the other hand, if the global "Surround Sound" switch is set to "Dolby Surround," then my primary AAC audio track is output as stereo AC3 mapped to DD5.1 channelization and my secondary DD5.1 track is mapped to all 6 channels. Lastly, the global "Surround Sound > Stereo" setting outputs both my stereo AAC and AC3 DD5.1 audio tracks as Stereo PCM. In all cases, applicable receiver "Effects" settings worked normally. As a final test, I sourced some HiRes (24-bit 192.0 KHz) WAV stereo PCM audio files through the same TV4 global "Surround Sound" settings with the same results—i.e., the global setting determining the output compression format and source channelization determined the maximum possible number of channels mapped to the surround output format. However, it is still unclear if source PCM and AC3 source content is "passed through" natively or if all audio is "converted on the fly" by the TV4 to the user's targeted global "Surround Sound" setting and if so, what sampling settings are used.