The thing is, for season sets, airdate order is the general standard. Most shows, people wouldn't even notice. Star Trek, though, has the big old fan base. Also, the series visually evolved over the first half of the initial season, and had episodes scheduled based on whether or not the effects were finished. But since the series isn't serialized, it didn't really matter. I think only die hard fans care all that much. If they put Trek in production order on the season sets, it would be one of the few that did it. Yes, I know, Firefly was changed to production order, but that's because the series was kinda serialized and the aired order made no sense at all. As a kid, as much as it was apparently run in production order, I still remember noticing Uhura's uniforming changing from red, to gold, to red for a few more episodes, and then gold one more time. So, at some point in the NYC area, it was run either in airdate order or just jumbled.
Now, if TNG were released in production order, you'd have Tasha Yar in an episode after she died and the second part of "Unification" placed before the first. Or Deep Space Nine would have had "Through the Looking Glass" between "Probable Cause" and "The Die is Cast."
So, while there are exceptions, original airdate order is the norm for box sets.