Maybe I'm just not trying hard enough...
Even among the Lominsan standard, there are a few giveaways. All three ships in the second serpent appearance use diagonal red sails and fly 'Cuda flags, as does the one Commodore Sthalmann is commissioning in Treasures of the Main.
However, Hob's ship clearly has a few differences. There are no cannons, the sails are white, he flies no flag. These qualities seem to be a little rarer in Limsa. However, Sthalmann's ship in Shapeless Melody is quite similar, though the sails are tied to prevent damage.
That means ... unless there are any other ships in Limsa that meet these qualities...
HUH. Well, shit.
Like, the Astalicia...
Back to where I started with my theory above then - one or the other.
To some degree, her mission in Lominsa is quite different than just figuring out how they'd fare against the Empire. In the entire time she's in town, the only question she makes as to the Garleans or Lominsa's ability to defend against them is, "What of the Empire? ... Surely they would not attack an independent city-state this far south." and that's it. She spends the rest of the time inquiring about "shadowless associates," Ascians, and the Key (Treasures of Swallowtail Roam). She doesn't even realize until halfway through that it could be used to summon an army.
For starters, Ferne's confirmed that the sea serpent is not by any means Leviathan, but, like Midgardsormr, an independent great beast with a mythology rooted in The Twelve. This makes sense, I guess, because he doesn't bother stopping to demand aether, bask in the worship of his cult, and give a lenthy diatribe about how unworthy and insignificant everyone else is.
By this point in the story, I'm pretty sure that the Seal Rock expedition's destruction is well over with. After Emerick sold out the Seal Rock unit, he was arrested by Sthalmann and sequestered at sea (where they hide criminals they think will be assassinated in Coral Tower). This was probably just to keep him safe until he could be spirited away by Sthalmann again, seeing as how he fully expects to be let out and stages a fight with Merodaulyn to make it look good.
How does the player end up in this? In an echo, he hears that Emerick was sequestered at sea and demands to be brought to the sequestered ship, despite people at the Wench telling you he's dead. Baderon calls in a favor from Hob, who for some reason borrows a ship from the Fisherman's Guild to bring you out there. On the ship, Hob spies some Serpent Reavers, which for some reason triggers an Echo where Travanchet attacks the sequestered ship looking for Emerick and the serpent shows up to trash everything. Why exactly Hob would have anything to do with this is something I'm still working on. However, Y'shtola shows up to warn Emerick that the Ascians are after him, and Merod says that if she's here the 'Cudas can't be far behind. They're not - two more ships show up to take on Travanchet's boats, but everyone loses. The boats are trashed, Merod disappears, Emerick seems to get injured pretty badly and eventually become Blackburn and Y'shtola... arrives back in town like nothing happened (again, making me think maybe she's able to time-jump somehow. Hey, Lou did it.)
This one gets under my skin a bit. Sthalmann's plot killed the admiral of ten years ago - and now we have Merlwyb. BUT - despite the fact that NPCs refer to her as "the new admiral," more NPCs and quests make it clear that a new Trident is fast approaching. It's the crux of the MRD storyline - the Trident is coming and the crews are trying to get the upper hand on one another.
These aren't just pre-GC leftovers, either. One NPC in town states:
"Pirates in an uproar over the new Admiral? Hah! If they don't like her, then all they have to do is beat her in the next Trident. If they can't do that, then they should crawl back into their holes and keep quiet until they grow the stones to stand up to her!"
So, it's on a schedule of some kind. I'm not sure what that schedule is. There's also the possibility that there was an admiral BETWEEN the one who died in 1562 and Merlwyb. This would make sense, since she'd be the winner of the most recent Trident ("the new admiral") but the next Trident approaches.
This I agree with. Like I said, it bothers me that the only way I can think of to cram it together relies on making assumptions like this - there has to be something I'm missing, and it's possible that, like the "seal" under Silvertear, we just won't be aware of it until the game or devs say so.
The way he calls out orders aboard the ship he's on in Shapless Melody does make him out to be an important figure on the ship. However, this creates a circular problem in your logic as much as it does mine. If he's commodore but undercover, then he should command so much authority on the ship -- unless people know he's commodore, and then why is he in civvy gear with no title?
It might be a combination - at that time he's a first mate aboard a pirate ship (as we've seen, maybe even the Astalicia)