The fact that a Lt. Cmdr. could be made the CO points to the fact that it was primarily considered a support vessel. I don't know that we ever see it operate far from Federation Space, the way the Enterprise did, without being part of a fleet.
Current day ships don't all have Captain's as the CO, our (our in the UK) Type 45 Destroyers have Commanders in the Captains chair (though previous commanding officers have held the rank of Captain) and some US Arleigh Burke Destroyers I have read about have Lt Commanders and neither of those I would consider a support ship.
Ships like the Defiant (and anything of similar size like the Saber and Nova) I could see being given to Commanders or Lt Commanders especially for patrol assignments, short term missions or when operating out of a home base (kind of like the Defiant).
Not all ships require a Captain and neither do all missions, plus some of a lesser rank can step up to the centre seat when the need arrises like Worf and Dax and Riker when he was promoted (and showed he could do the job) in BoBW.
It's not really the type or role of the ship that determines this but the size of the crew. IOW, how many levels of hierarchy are needed to operate the vessel. A small crew means fewer levels. On one ship I served on - crew of 450 commanded by a Captain - the ship was divided into departments (CDR or LtCDR), which were divided into divisions (LT, LTjg,or ENS), and the divisions into smaller teams (E5-E6) based on various criteria (E-Division had a electrical repair shop, tool issue shop, CCTV room, phone repair shop and gyro room.) I also did reserved duty on a minesweeper-type vessel*, commanded by a senior LT, where the entire crew was about a dozen guys. No levels at all. And a lot of cross-training.
*(a converted Academy training boat, using sidescan sonar.)