So I am speculating this happens because of using Ogg Vorbis.
I don't know if the effect is intriduced while mixing the
6-channel file (I doubt that), or only when playing it back

AFAICT it is introduced when mixing the 6 channel file (FWIW ffmpeg exhibits the same behaviour).

In a freshly merged 6 channel file, I've tried remixing the channels into a different order with the result that both the original LFE channel and the new one sound "filtered" and have lost data.

Remixing a 7 channel file down to 6 channels also introduces the effect on the 6th channel.

p.ota.to