Apple TV 4K – Audio output question regarding lossless formats

it seems like the audio is decoded internally and sent out as LPCM instead of being passed through untouched.

Correct. LPCM decoding is lossless though, so it shouldn’t matter (much). LPCM can handle multichannel up to 7.1 on the Apple TV box (and optionally Dolby Atmos).

Is there currently a way to configure the Apple TV to pass audio through “bit-perfect” over HDMI — without internal decoding? Or is LPCM output the only available option?

There is no passthrough option on the Apple TV box (with current system software). This is intentional on Apple’s part. You have to choose between Auto (multichannel LPCM decoded), Dolby Digital 5.1 (downmix), or Stereo (downmix). The latter options are intended for fallback for compatibility, for setups that can’t handle multichannel LPCM.

One caveat is that Dolby Atmos decoding on the Apple TV box currently requires that it is embedded in a Dolby Digital Plus stream. Embedded in Dolby TrueHD, it can only be decoded to surround sound without height effects. Same for apps that can read DTS-X: the surround sound can be preserved, but 3D immersive (height effects) aspect will be flattened to the ‘bed layer’ through the Apple TV box.

This shouldn’t matter for commercial internet streaming, but will influence certain downloads and/​or extracted media that uses these latter audio formats.