Is there any reason for this oddity?
When the VHS eps were coming out, one set of releases was in production order. Lots of reviews were from people who'd watched first-run TOS in the 60s and many were wishing aloud that they could have had the episodes arrive in airdate order,
so they could re-live the experience of watching them as they were first shown on TV in the US.
The team who put out the DVD sets were also of that era, so they made sure the eps were in original airdate order. Sit with the old Ballantine "Star Trek Concordance" on your lap, spin the wheel on the cover, and read along with Bjo Trimble while watching the eps!