I have an idea: why don't you tell us how it works in detail, then if it really is "overwraught", we won't be complaining. It sounds crazy, I know, but providing enough information to allay peoples's concerns might, just might... allay their concerns.
If you don't want "guesswork and assumptions", then replace them with facts.
I mean, look at your initial post of the thread. Look how much it talks about NPCs "are tired of being shoved into tiny cubicles or L shaped tubes and they want you to know this!" That's a pretty direct statement that this feature exists to prevent that. So when you go on to say "NPC's are happier when they are not overcrowded with other NPCs ", the natural assumption is that "tiny cubicles" == "overcrowding".
If that's not what the feature is doing, maybe you could describe it more accurately.
That's kind of irrelevant, since you have to make an NPC happy to get a Pylon for a particular biome to begin with. The issue here there is how you acquire Pylons, not how you use them.
Or more to the point, the issue is linking happiness to fast-travel.
Wait, it is? I mean, it wasn't before. Or at least, not like this.
Defending against the spread of CC was just... don't go to those places. That's how you defended against its spread; ignore it. If it is getting close to your town, you built a moat to keep it out, a gap too big for it to cross. You only need to directly defend against it if a patch of it happened to enter your quarantine directly.
The Clentaminator and such were tools for attacking the infections, for eliminating them from a specific area. Not for defending an area from them.
At least, not until now.
I don't much like the idea of having free fast-travel impacted by the rapid spread of early hardmode infections. That sounds like adding a lot of busywork to a section of the game where we're already busy. At that point in the game, I should be exploring underground, looking for hardmode ores and surviving hardmode enemies, not doing upkeep on my fast-travel network.