I disagree.
Starfleet Command, is synonymous with either Starfleet Headquarters (ie the Pentagon) or is shorthand for the Starfleet Command Council (ie the Joint Chiefs or more likely the Military Section of the UK Defence Council) for the simple reason that such an element must exist and its the most viable term to use for it.
Back in the ENT era, we are shown that the "Fleet Operations Center" is the Starfleet Command building.
Given we have a few disparate things, "Starfleet Command", "Starfleet Headquarters", "Fleet Operations" and "Fleet Operations Center"... I don't think we are far off from each other here, just some nomenclature issues.
To me, from what we have seen,
"Starfleet Command" is the overarching parent organization of all the divisions/branches of Starfleet. I agree that "Starfleet Command" is essentially the "Command Council" or whatever you want to refer to it as.
"Starfleet Headquarters" is the physical structure/grounds, i.e. the Pentagon.
"Fleet Operations Center", from ENT "Demons" and VOY "Non Sequitur", is a
part of Starfleet Command. The Starfleet Chief of Staff has an office at the Fleet Operations Center.
"Fleet Operations", would logically be the organization that people in Starfleet Command's Fleet Operations Center command.
So... Starfleet Headquarters is the physical location of Starfleet Command, a part of Starfleet Command is the Fleet Operations Center.
No, he was Starfleet Intelligence later and Exploration Corps or if you insist Fleet Operations first (he was a starship commander), and invokes the name and authority of the Chief of Starfleet Security to reinforce his orders:
PRESSMAN: Well, this time we may have a chance to do it the right way. If this mission is successful, if we find the Pegasus and the experiment, we can finish what we started twelve years ago.
RIKER: You want to try again?
PRESSMAN: It's not just me, Will. The Chief of Starfleet Security has personally given me her assurance of complete support.
RIKER: Admiral Raner? How many other people know about this?
PRESSMAN: Not many, and it's up to us to make sure it stays that way. Raner has given me written orders for you. You'll find them coded in the Enterprise computer. You've been instructed not to reveal the true nature of our mission to anyone else, not even Captain Picard. Will, don't worry. It won't be like it was twelve years ago. And this time, no one's going to stop us.
Which suggests that ADM Raner is the direct top-level authority for one of them, and logically it's more likely to be Intelligence flag officer Pressman rather than starship officer Riker.
I think we are interpreting this far differently.
Pressman was stated to be Starfleet Intelligence at the time of "The Pegasus".
Now i'll say perhaps that Pressman was not actually a member of Starfleet Security, it's just noted that Starfleet Security developed the cloaking device. So he may well have been Exploration Corps that was simply working with Starfleet Security.
But in these quotes, Pressman... being explicitly "Starfleet Intelligence", then says "It's not just me", and he has the assurance of support from Starfleet Security.
To me, that sounds more like Intelligence and Security are working together on this matter, not that there are one in the same. Pressman isn't 100% sure that Riker will trust him directly. He COULD go ahead and order Riker himself, but... Pressman knew there was a chance that might end well. The phase cloak was also Starfleet Security's project and property, so the Chief of Starfleet Security giving Riker written orders makes the whole thing seem more legitimate (in theory), rather than Intelligence Admiral Pressman going on some rogue mission to fix a past mistake.
I don't really have any direct issue with Starfleet Intelligence being a subordinate organization to Starfleet Security... it makes some sense for them to be linked, but i'm just not convinced that's how its presented.
On the other hand, thinking about the relationship of the Expeditionary Force... really digging deep into Starfleet departments and what not, there is a big part of me that wants to adjust my org chart a bit and rather than have it be it's own branch of Starfleet directly, break out Starfleet Tactical Command into it's own branch, with the Expeditionary Force under that command.
For my purposes, i'm keeping "Fleet Operations" as the command for, well, fleet operations. In-universe, it's by far the largest of all of them and when someone refers to "Starfleet", they're usually talking about some flavor of Fleet Operations, although the term could technically apply to anything. (Saying "Starfleet Fleet" sounds redundant, but it's one of those things that results from holdover terminology from the past. Earth Starfleet was just Earth Starfleet. As it ballooned under the Federation, the old name stuck but needed to be expanded out.)
I'm still really on board with the Lower Decks support fleet being a part of Fleet Operations Support. Looking into that alittle, Fleet Operations Support has the authority to give orders to starships. It's really not unreasonable that they have their own fleet under their command to do so, rather than commanding Exploratory Corps ships (or other things).
I think there would be other divisions under "Fleet Operations", so far it's "Deep Space Exploratory Corps" and "Fleet Operations Support". I'm thinking there is a department designation for intra-Federation patrols or what not, the ships we don't hear much about that putz around Federation space doing nothing exciting.
I like to think that in the Discovery-Era, Enterprise was Exploratory Corps, but many of the other ships we see in Discovery are a different command. I also think these departments could change a bit over time, with the Exploratory Corps being a much larger organization post-Khitomer Accords.
Maritime Operations (informally the "Marines") which focus on "the cold and wet" operations ie sea, polar, and mountain operations.
Air/Space Operations (informally the "Paratroopers") which focus on air support, base security and EVA/OSD insertions in contested areas.
Desert Operations (informally the "Commandos") which focus desert and other "hot and dry" environments.
Recon/Mobility Operations (informally the "Rangers") which primarily the Force's Intelligence, Surveillance, Target Acquisition, and Reconnaissance (ISTAR) component but also support Starfleet Security forces in urban and station security operations not requiring EVA/OSD capacity.
I feel like it's a bit more in the spirit of Starfleet to not really have a separate command for these things, but they would have people specializing in certain environments.
"Marines", in context of here, is holdover past nomenclature. They're not specifically amphibious units meant to storm beaches. It's more of a nod to "soldiers being transported to combat on ships and working closely with the "Navy"".
I do particularly like the Desert troops being called Commandos though... in my own backstory I have established for this, in the earliest days of the "Marines" it was specifically Vulcan Commandos who formed the core of desert combat operations given their home environment. It's fitting that the title of "Commandos" continued on in that tradition.
Tangentially related, i'm reworking some of the backstory of the specific alt-universe and tweaking some things. I initially had Daedalus-Class ships showing up post-Romulan War, but i'm tweaking them to have entered service during the war. They're not quite the Daedalus of canon, but close. They're small and meant to be manned by a small crew, a dozen people tops. My new backstory for them is that Tellar, Andor, and Vulcan are getting pummeled by the Romulans, Earth is trying to ramp up production and get ships out to help but they're behind the curve. The Coaliton members reverse their stance on Earth and send engineer observers to help integrate their technology into Earth designs.
They come up with the Daedalus, which is pretty much a flying Space Tube with a Warp 5 Drive stapped to it that proves to be fairly inexpensive, Earth can pump them out with their existing infrastrure fairly quickly, require small crews and use most of it's internal space for weapons (nukes, in this timeline). They're cheap to build because they're glass cannons, held together by Space Duct Tape (or, rather, Frankensteined Vulcan/Andorian/Tellarite shield technology). They also helped with simplifying the production of warp drives so these ships could actually make it to the battle in a reasonable time frame. The Daedalus was easy enough to build that the other Coalition members started to produce them as possible, although by the time they enter production, Vulcan/Andor/Tellar are in very rough shape and barely holding on.
As it relates to the Marines, when the dust settles, the Federation forms and things get back to normal, the Daedalus-Class ships are largely retired... they were never intended to have longevity, they were built to be almost disposable. The fairly early Marines end up with a stock of would-be-decommissioned Daedalus', which form the majority of their early paltry space assets (mostly just used as transports, the missile bays mostly gutted and converted to troop transports).
