Does it?
If you have 8 Pylons in the world, figuring out which one the Dryad is at takes more than 2 seconds. You have to search through the map (which may be rather big), looking at every Pylon location until you find her.
I don't know what you mean by "NPC prison", but my bases are designed for easy navigation from room to room.
When I said that this mechanic had no "depth", I was referring to the gameplay depth, the mechanical complexity of the actions the player takes and the variety of choices the player has. I don't care if this mechanic allows an NPC's personality to be imposed on the gameplay. What I care about is how that imposition affects the gameplay.
From a gameplay perspective, this mechanic is exceedingly shallow. Every NPC has one or more preferred biomes. They have one or more un-preferred neighbor NPCs. And you can find out about any/all of these... by asking them.
This has all the complexity of a game of Go-Fish with all the cards face-up: just pair the ones who match. Problem solved.
So where's the depth?
I've never played this game. However, I imagine that, from a gameplay perspective, "making friends" with them requires more effort than just asking them their preferences and moving them to that preferred location, right?
Because that's all Terraria is bringing with this change. There's no "sense of accomplishment" to be had for a task that is rather trivial.
For you, a specific game feature was able to inspire you to consider what might be an interesting home tailored to an NPC. That's great for you, and I mean that sincerely.
But do not mistake a source that managed to inspire you as being the only possible source for similar inspiration for others.
There is nothing that prevented anyone from previously coming up with those ideas. In fact, I rather suspect many people have used these ideas to varying degrees previously. This feature is not empowering you to do something you could not before; at best, it has inspired you personally. But that's just you, personally.
Creativity, or a lack thereof, is not why people don't commonly build these things in their runs through Terraria. It's because, as I have stated before, NPCs are game mechanics; they exist for the player to be able to use them. And the most convenient way to use them is if they are all right there next to each other.
If you play Terraria for long enough, and are trying to just experience the content of the game, NPCs are just a means to an end. So you spend the bare minimum of time on them that the game requires and you move on. And people will continue to do that in 1.4.
All 1.4 did was change what that bare minimum would look like. Instead of one set of boxes, you have several. But they'll still be cookie cutter, minimum effort boxes, because that's what it takes to get to what they feel are the good parts of the game.
You can only have one active spawn point. I picked the Dryad as an example because, by and large, you only rarely need her services. If your bed will only be near a couple of NPCs, you won't pick the Dryad as one of them.
I can get used to a lot of things. You haven't explained why I should have to get used to it. It's not improving my play experience. Or at least, not in a way that couldn't easily be achieved in another way.
The question you're not asking is why people build these so-called "commieblock towers" in the game. You seem to think of it purely as a stylistic choice. It's not.
It's a choice that favors player convenience. It allows me to see the greatest number of NPCs all at once, and to quickly and efficiently access them if I need to. They're right there; I don't have to go looking for them, or activate a Pylon or whatever else.
But that's kind of the point. See, the correct way to deal with cheese strategies against the Moon Lord is not to make the Moon Lord arbitrarily invulnerable to cheese strats. It's to not put cheese strats into the game. I mean, Vampire Knives. That doesn't even rise to the level of a "strat"; it's just a weapon you pick up that turns the game into easy mode. If you put an easy-mode weapon in the game, it's silly to give the final boss a "you can't use the easy mode weapon against me" ability. It's a bait-and-switch: you teach the player to use easy-mode, then you take it away when they need it the most, forcing them to learn all the stuff they didn't learn when they were relying on easy-mode.
Your analogy is good, because this feature comes from the same kind of thinking. This mechanic feels very artificial, something bolted onto an existing system in order to forceencourage players to play in a way that isn't necessarily how they would play otherwise. The devs don't like people making tight-knit homes for NPCs, so they hurt you if you play that way.