It's not me doing anything wrong. It's not me having misunderstood something.
Please only respond if you know what is going on for sure.
"To the Left" "To the Right" ??? To me they appear as above and below. So which is which?
The "Match Sequence Settings" settings forces Pr to use rendered preview files as a source, instead of the actual source video. If no rendered preview files are present, it defaults the export settings to the same settings that are used in the sequence to generate the preview files. Check your sequence settings - you'll see what export settings Pr is using when MSS is selected. Most likely, it's not what you want or expect.
I've been told that the Match Sequence Settings check box is working as designed. I personally think it's confusing and misleading.