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I'm sure we're all aware that Magas Volar is not physically accessible in Morrowind, except by using a certain amulet found only in Tel Fyr.

And we know Boethiah's original shrine was abandoned long ago and submerged underwater. But not only is his statue down there, but a whole Daedric ruin is half-buried around it, completely inaccessible from the outside.

Since there's no way to enter that ruin's interior, and there's no doors connecting the interior of Magas Volar to the outside world, I'm willing to assume that Boethiah's Daedric ruin and Magas Volar are one and the same. Is it any wonder how the Tamrielic Empire wasn't able to find the last of the Daedric Crescents when they were rounding them all up? Because it's hidden inside of a ruined Daedric shrine, which was abandoned long ago by even its own worshippers AND trapped beneath dozens of fathoms of water. The fact that the Magas Volar chamber where you fight Lord Dragas Volar isn't at all flooded is because that particular chamber has no openings of any kind, and the only way in and out of there is teleportation.

And according to this very Wiki, the early versions of TES III: Morrowind allowed you to respectively teleport out of there with the Almsivi or Divine Intervention spells to either Vivec City or Pelagiad, both of which are fairly close to Boethiah's Shrine. Yes, there are certainly Intervention-friendly locations closer to Boethiah's Shrine, but we know how inconsistent those warp points can be (like how Divine Intervention sends someone in Seyda Neen to Pelagiad, even though Ebonheart's arguably closer.)

The Daedric Crescents were artifacts of Mehrunes Dagon, not Boethiah. The sunken shrine is more likely to be an extension of Ashurnibibi than Magas Volar.