This... is exactly what I wrote in the second half of the first paragraph... Yes, this is exactly how they'd need to do it, if they were to refurbish Ishgard. Hence my potted plant example. Alexander is another example. Before you get the cutscene where he rises from the lake, there's a rock formation where his hand is going to be planted. Can't walk on it before, can't walk on it after. Ditto his other hand - and before you unlock the Creator, there's a chunk of rock you can stand on up in the shield where his head pops out.
And yes, I also wrote words to the effect of "way more effort than it's worth" (the stuff about what SE's willing to invest). So you and I are in agreement there, as well. The purpose of my writing was to show that it was feasible, not that it was likely to happen. So, yeah, you spent your first two paragraphs agreeing with and repeating what I just wrote.
Since you apparently think that the Haukke Manor example wasn't enough, how about Hullbreaker Isle? You know how new players running Hullbreaker Isle are all confused because this lost island has all kinds of Maelstrom-built fortifications on it, and training areas for battling wild beasts right? Of course you don't, because that doesn't happen. New players running Hullbreaker normal don't see these things. Hullbreaker normal and Hullbreaker (Hard) are two different instances. They exist comfortably side-by-side.But having an instance be something completely unrelated, taking all the meaning out of actually running it later on? That's ruining stuff for the newer players.
Haukke Manor was filled with imps and skeletons and all kinds of voidsent, just the way it is during the actual dungeon. Saying "We sneaked around in a haunted house but didn't fight the monsters there" and later returning once you hit lvl..27 or whatever it is, to now actually slay the creatures that during the event you could just sneak past because you were still just a little beginner? That makes sense within the narrative.
The same can't be said about seeing a freed and cleaned up Dun Scaith City being readily available to everyone only to THEN be told "Oh btw, go clean it up, it's this unknown place filled with monsters that no one has ever reached!". See the break in logic?
You can argue that adventurers who have been to that place liked the look of it and tried to recreate it on the ground when they built their new housing area, but the OP asked what will/should happen with the place itsself, not a copy of it or something like that. And people moving into content that will still be relevant to someone down the line does not make for a good..well, anything, really. Because anything that is publicly available there breaks the story if it's available before clearing said content.
This game's Hard Mode dungeons show that SE is willing to update places to show what has become of them after the players initially ran them, and as far as I know, no players have any issue with this. Players find it perfectly acceptable to go back to Halatali and find that it's been cleaned up and converted into a gladiator-style training area and arena. There's no break in logic, because no one can see the clean Halatali until they've seen the dirty one. The same would be true of Dun Scaith.
So, the insistence that the OP must mean that they need to set up houses RIGHT THERE in the same area that newer adventurers are adventuring through is nonsense. A new instance patterned on the old dungeon, accessible only after the old dungeon is completed, is perfectly fine, and something that has already been done in this game time and again with EVERY hard mode dungeon. The only change in this case would be that the new instance is a housing area instead of a new dungeon.
The fact that you'd only be able to access Dun Scaith housing after completing Dun Scaith is the biggest reason why I don't believe it would happen. That's too restrictive a requirement - and if they simply ignored the requirement, and let folks march into Dun Scaith housing at level 5 (the same point in development where they could access the other housing areas), it would be simply ridiculous, just as you say. I don't think ANYONE asking for housing in Dun Scaith is suggesting you should be able to enter it at the same time you can enter any other housing area.
Seriously, though, housing that you can only access late in the game may be just what the doctor ordered for many of the problems facing housing. Folks complain about players buying houses with their low-level alts - well, now, they'd need to get their alts most of the way through Heavensward before they could buy up the properties. Ditto for RMT buying houses, if RMT buying houses is even really a thing.