DiscardPadding lost during remuxing
the Matroska specifications allow the DiscardPadding element for any track, not only Opus. And some of ffmpeg's encoders already produce such tracks (or more exactly, they already add the AV_PKT_DATA_SKIP_SAMPLES side data to the packets at the end which ffmpeg Matroska muxer translates into DiscardPadding in Matroska), such as the libmp3lame encoder. The problem is that this DiscardPadding is lost during normal remuxing; the generic passtrough packetizer keeps it. This probably happens with all other non-generic, non-opus output modules, too.
I have uploaded mp3.with.DiscardPadding.mka to your server.