Given what Jefferies said about the purpose and nature of nacelles, I doubt any faster than light warship meant to be taken seriously, but also on something of a roughly equal technological footing as Enterprise, would NOT have had nacelles. It would have had nacelles, and they’d be far removed from the inhabited areas of the ship.
We are never told the Romulan bird of prey is limited to impulse.
Kirk: ”Can we engage them with a reasonable possibility of victory?
Scott: No question. Their power is simple impulse.”
Kirk: Meaning we can outrun them?
Scott says the POWER is simple impulse. Kirk is left questioning whether that means their SPEED is less than Enterprise. And that question is never answered because Stiles goes off on a rant. Plus, we don’t know if any observed limitations to the bird of prey are confined to how it operates under cloak. Spock says as much when he describes how the cloak would work - “Invisibility is theoretically possible, Captain, with selective bending of light. But the power cost is enormous.”
From the designer’s perspective, we know those are nacelles. They look like Enterprise’s nacelles, and for good reason. The script said the bird of prey was a stolen design. The designer would have designed to the requirements of the script.
As for Mudd’s ship, what was seen was a blob without discernible form. Lazarus’ craft is a tiny, one man, interdimensional pod. We don’t even know if it travels in real space or instead gets from place to place through a dimensional void. Botany Bay is “launched”, “atomic” powered, and dates from 1996. And Fesarius is shown in every way to be alien and almost incomprehensibly different. In other words, there is no opportunity to show a ship design before “Errand of Mercy” with nacelles other than the bird of prey. One is out of viewing range, one is not even a spaceship, one is wildly old and primitive, and one is wildly alien.
As for the TSFS mess up over their “bird of prey”, with a Romulan design being fitted with a head and boom to make it look Klingon, it may have had precedent. The back half of the D7 does - sort of - look like the original, Wah-built, Romulan bird of prey, turned upside down and backwards. It’s possible Jefferies designed the Romulan ship as well, with this “manta” look in mind, and we just have never seen his sketches.
https://i.pinimg.com/736x/c7/b2/cd/c7b2cdec33091ee481b368499781a260--ishigaki-manta-ray.jpg
As for your design Warped, you might want to give it a very subtly discernible “head” by just barely slimming the “neck” to imply something of a boom. That would be a little hint while not being overt - implying an evolution in Jefferies’ thinking was at work.