Blurays with plain TrueHD or DTSHD tracks get unpacked to raw mulichannel LPCM and are lossless... What is lost is the height channel metadata if it is an TrueHD ATMOS or DTS:X track. You still get the lossless base TrueHD or DTS-HD in raw PCM though... it isn't sent as lossy DD+.
Data source?
From Technical Specifications:
HE-AAC (V1), AAC (up to 320 Kbps), protected AAC (from iTunes Store), MP3 (up to 320 Kbps), MP3 VBR, Apple Lossless, FLAC, AIFF, and WAV; AC-3 (Dolby Digital 5.1), E-AC-3 (Dolby Digital Plus 7.1 surround sound), and Dolby Atmos
No mention of PCM, TrueHD or DTS-HD.
From Infuse:
Infuse does support DTS-HD MA and TrueHD, and the full lossless audio will be sent to your receiver as LPCM.
They can do it because they are using their own code and have purchased the appropriate licenses.
"There is currently no support for DTS audio on Apple TV hardware."
I can't get DTS sound to work on my 4K Ap… - Apple Community
"Apple TV 4K doesn’t support Atmos TrueHD natively. Instead Apple TV 4K supports Atmos Dolby Digital+ for input, as that is what streaming services use."
Does the ATV 4K support TrueHD Atmos? - Apple Community
Since transcoding generally results in quality loss and we don't know the ultimate bit rate it's hard to tell what the native player does.
Do you have a receiver which displays the apple TV output audio bitrate? I haven't been able to confirm what happens during the conversion since Apple TV won't play MKV's which have the full audio with the native player. Do get better results with Plex, Infuse, or of course NVidia Shield which plays the tracks without any conversions