[curiousnoob]

What audio codec are you playing ?  (Dolby Digital / AC3, Dolby Digital + / E-AC3, DTS, Dolby True HD, DTS HD Master Audio, DTS HD High Resolution Audio, FLAC, AAC, PCM etc.?)

What audio codec does your AVR say it is receiving when you have passthrough for that codec enabled and when you have passthrough disabled?

if you have proper passthrough enabled then it's not really possible for the Pi to alter the audio channel mapping - as it is simply 'passing through' the compressed multichannel bitstream from the source file untouched, for the receiver to decode.

Are you running LibreElec or Kodi under Raspbian. 

I tried various codecs. If pass through is enabled my receiver displays them (DTS, DD, DD+,...) When passthrough is diabled it shows PCM only.
Problem occurs both with and without passthrough enabled.
I am runnnig a headless Raspbian buster (lastest) with Kodi 18.6.

@Puck: looking forward to the 18.7 to see whether it will be fixed.