In "The Deadly Years" when Commodore Stocker takes command of the ship, it's only because Kirk has become incapable of command. It's a desperate situation that leads to the Commodore taking action (although he's obviously not a starship commander by trade).
Yet, "The Doomsday Machine" and "The Ultimate Computer" present us with Commodores who are seemingly in actual regular command of their ships: Commodore Decker of the USS Constellation, and Commodore Wesley of the USS Lexington.
We might excuse Wesley as being another unique situation, as they're testing out the capabilities of the M-5 in a battle scenario. Maybe he's only the temporary commander of the Lexington for the purposes of that particular test run.
On the other hand, the script of "The Doomsday Machine" basically assumes that Decker is the proper master of Constellation, that he is the captain except for his rank. Unless we are to assume that the Constellation's own captain died and Decker (like Stocker) simply happened to be on-board and took command?
I think Stocker was an exception due to an emergency situation, he had never commanded a ship and it is implied that is outside his normal career specialty.
Decker does indeed seem to be CO of Constellation
and no other vessels. Wesley seems to be Lexington
's CO as well as task force commander.
My usual pet explanation for the situation is that starships are organized in divisions (or squadrons if you prefer) of three or four ships. The captain of one of them has the rank of commodore and is division commander on paper, but in practice the ships are spread all over space on different assignments so the division command doesn't come into play very often. Wesley could be an example of the division commander actually taking command, but an oddity is that he wears the Starbase/Starfleet Command badge.
Side note: Decker would not be "master" of Constellation
, that term applies to captains of merchant ships.
What's the real-life protocol in these situations? Was it ever common in the real navy for a ship's regular "captain" to actually be a commodore?
A bit of a complicated answer. In the olden days, the British navy divided commodores into first class, who had a captain under them on their own ship, and second class, who were captain of the ship as well as the squadron. So one was like a junior admiral, the other like a senior captain, but both were really captains with a temporary jump-up in rank, and both always had command over more than one vessel, which was the whole purpose of the rank.
The early US Navy, small and lean, used the "second class" commodores extensively. Como. Preble, who made a great reputation for the USN in the Barbary Campaign, was captain of Constitution
as well as squadron commander. Thomas Truxtun, the "star" captain of the Quasi-War with France, had refused the command because the Navy Department wouldn't assign a captain under him for his flagship.
There was a time after the Civil War when a few USN commodores (a permanent one-star rank, by then) were assigned command of large warships, without an associated squadron command. This was mostly an aberration caused by the numbers of senior officers created for the war, and after the navy had down-sized in the 1870s it didn't happen any more.
^ I think in a real-life situation an Admiral wouldn't be "on the pulse" during such a command. Traditionally he'd be given his own command centre and would liase remotely with the main bridge, but to take the TMP situation as an example, Kirk would be in his quarters or an office on another deck or something, and not actually on the bridge (that'd be Decker's job).
That is correct. The relationship between an admiral and the captain of a flagship, in theory, is supposed to be the same as with any other captain of the command. The admiral and the staff live, eat and work apart from the ship's personnel, and the admiral gives the captain the courtesy of notifying him in advance if he wants to leave flag country and enter the rest of the ship. As you say, not great for dramatic interplay.