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If you check the log file you'll find the script MeGUI uses for downmixing the audio. It reduces the volume to prevent clipping when the channels are combined, followed by Normalize() to increase the peaks to maximum after downmixing (assuming the Normaize option is checked).
Maybe ffmpeg doesn't prevent clipping by default, and likewise when you playback 5.1ch audio being downmixed to stereo, the volume isn't being reduced to prevent clipping either, so they sound the same.
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