And an actual flight team to handle small craft operations (with maybe even a flight or wing commander on ships with a large complement of small craft)?
Who's to say there wasn't? Lt. Latimer in "The Galileo Seven" may have been part of it.
The Chief Engineer being in charge of ship's security made zero sense, otherwise, and that's just the most blatant example.
It would make zero sense, but the security chief was a different person as seen in "The Devil in the Dark."