I don't really like to say this as a reason, but I think technology might be a reason for Red Mountain to be taller now. It is suppose to be the tallest Volcano in the entirety of Tamriel and in Morrowind, it just didn't seem like that. But seeing as the Dunmer had to flee from Vvardenfell after this eruption if Red Mountain, I wouldn't bet on there being any dweller ruins being left in the close vicinity. They had to be covered by the ash and lava.
Yes, but I was surprised to see where Dagoth Ur was actually located, which lead me to conclude that Dwemer architecture cannot be destroyed by lava (though they can be made inaccessible and probably super heated), as being right in the crater of the mountain meant that the former Dwemeri capital must have been hit by previous eruptions and still survived. After all, you wouldn't build on Red Mountain if your buildings would be damaged by an eruption.
Anyways, that has nothing to do with this thread. I do believe that fort shown must be Frostmoth if only because there are literally no other forts on the island. I wonder where Miraak temple is though (I thought either the sunstone mound or the altar of thrond for some reason).