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In DS9 "Adversary" Sisko is promoted to Captain.
As a side note, wouldn't a Captain or higher level officer be present to present him with his pen and give him his new rank?
You are confusing the title of captain with the rank of Captain. The difference is referenced in the opening paragraph of the Memory Alpha article Captain:
Captain is a military rank, the equivalent of which was used by the service organizations of many civilizations. The title of captain was often used by vessel commanders and, as a naval rank, in many Earth navies and Starfleet, was above commander. As an infantry rank, captains ranked subordinate to a major and above a first lieutenant. The abbreviation for captain was capt.
While that can be one and the same (especially in the Star Trek universe), the title of captain is given to the commanding officer of a vessel, whereas the rank is given to an individual who was promoted from the previous rank (in Starfleet, it would be a promotion from Commander, as Sisko was).
For example, in Star Trek V: The Final Frontier and Star Trek VI: The Undiscovered Country, Captain Kirk held the rank of Captain and was also given the title of captain as commanding officer of the USS Enterprise. At the same time, Captain Spock was not captain of the ship (despite having the rank of Captain), but held the position of First Officer. Additionally, as user16696 reminded me, Scotty also held the rank of Captain by the time of the last movies.
Similarly, in Star Trek: The Motion Picture, Admiral Kirk was given command of the USS Enterprise so was addressed as "captain" throughout the movie because he was given that title as the commanding officer of the Enterprise.
The Defiant itself also illustrates this difference, although the distinction was not openly addressed until later in the series. When he brought the Defiant back to DS9, Sisko still held the rank of Commander, but when he was in command of the Defiant, he technically held the position of captain (although no one addressed him as such). Then, early in Season 6 of DS9 ("Behind the Lines"), Lt Commander Dax was assigned as the commanding officer of the Defiant, so was given the title of captain, and she was actually referred to as "captain" by the crew while she was in command. In fact, there is a dialog between O'Brien and Cadet Nog about this exact situation:
O'Brien: "It's an old naval tradition. Whoever's in command of a ship, regardless of rank, is referred to as 'captain'."
Nog: "You mean if I had to take command, I would be called 'captain,' too?"
O'Brien: "Cadet, by the time you took command, there'd be nobody left to call you anything."
So to address your question more directly, the reason Sisko was promoted to Captain was because he earned the increase in rank through his service to Starfleet and the Federation. It is not related to the Defiant at all, simply because he already held the title of captain every time he commanded the ship.
As a military man, I'd like to give some military feedback on rank vs position.
A Captain in Starfleet would be the same as a Captain in the Navy or a Colonel in the other branches. I have seen a Brigadier General take over Division with the expectation that he would be promoted to Major General during his command. The same for a Lieutenant Colonel that took over a Brigade, becoming a full Colonel.
With that being said, Deep Space 9 is more like having command of an outpost or a NATO base somewhere, and there really isn't a rank protocol for that.
Most likely, Commander Sisko was probably assigned to command DS9 because he was a competent leader and a Field Grade officer with both diplomatic and combat experience. His promotion was most likely due to: excellence of service, causing promotion over his peers; plain old fashioned time in service/time in grade (rank); or a combination of the two.
Commanding the Defiant wouldn't have had a direct impact on his promotion, since he was already the commanding officer of DS9 and the Defiant was assigned to DS9. In fact, he probably would have never actually commanded the ship from the bridge. As DS9 senior commander, he would have probably stayed at the Command Center, as a unit commander would stay at the TOC (tactical operations center), and play chess.
The best reason I can think is that he had proven himself, and that he’d resolved his issues with Starfleet and his career after the horrific events of the Borg invasion.
His tiff with Picard over the deaths caused at Wolf 359 and the death of Jennifer gave credence to the idea of him having problems with the chain of command.
That being said, by the end of season 3 he had pulled himself together, run the station well, developed a strong relationship with the Bajorans and discovered the wormhole, amongst many other achievements.
Not to mention at the beginning of season 1, DS9 was a posting at the end of Federation territory. It was considered a challenge a but non-essential posting, thus only a commander level candidate was needed.
But by the end of season 3, the Dominion are starting to show their colour, and the importance of DS9 as a stop-off point for the Gamma quadrant and a defensible point against the Dominion advance was becoming evident.
That kinda covers the 'Why' part.
As for doesn’t he need a ship, no he doesn’t. Scotty and Spock were both Captains under the command of Captain Kirk. Further, as Star Trek Online is quite often considered canon (given credence by the Trek reboot movie and the writers of Star Trek), Starbase 82 is commanded by Captain Ogen.
Finally, technically yes, but he is not the only one to command the Defiant. It is a station resource like the runabouts (which each have their own names too).
