It's just strange, that's all. That something could be a universally accepted standard for a quarter-century and then be all but completely reversed within a few years.
Plus there's the fact that I spent most of my life as a Trek fan experiencing TOS in production order -- seeing it in that order countless times in syndication, reading about it that way in all the references, getting the re-releases of the Blish novelizations published in that order, etc. So it's really jarring to have those decades of consistent precedent suddenly overthrown. Airdate order will never feel right to me.
And the "it's the way it was originally run" argument may work for a lot of series -- like TNG, where they shot "Unification" out of order due to Nimoy's schedule, or M*A*S*H
, where the production-order syndication run totally screwed up the chronology of when B.J. and Potter arrived at the 4077th. But it doesn't work for TOS, because the airdate order was not chosen for story
reasons. It was sometimes because the network wanted to lead with strong episodes -- they chose "The Man Trap" to open season 1 because it was a monster story, and chose Spock episodes to open the other two seasons because he was the most popular character by a huge margin -- and sometimes just because of production logistics, some episodes' special effects taking longer to complete than others and thus having to air later. There are certainly shows where airdate order is preferable, but for TOS it's completely arbitrary and has no benefit to the viewing experience. So I think it was a mistake for the makers of the DVD set to apply that "standard" in this particular case.