I would be extremely surprised if this penalty was anything larger than 10%. And the bonuses for doing it are probably going to be larger than the penalties for not, in terms of straight prices. That being said, this one time I started a world and within 10 minutes found 2 pots that spewed out close to 15 gold each. Sorry, got a little bit off topic. Most of the people who prefer to build a huge central area are probably not actually going to be too impacted by the penalties. This other time I had a pirate invasion happen and walked away with 2 platinum in less than 10 minutes. Oops, my bad, it happened again. Now where was I? Oh yeah. As someone who primarily puts all of their NPCs in the exact type of prison as described and poked fun at several times, I can honestly say that this is literally not going to affect me or my enjoyment of the game negatively at all. The feature for pylons didn't exist last time I built a mega base, and if I do it again after the new update, literally nothing changes except a "price penalty" that, as I previously estimated, is probably not going to be larger than 10%. I don't know anything about it, but I doubt it's going to be an exorbitant amount.
Now, the pylons. A mechanic that is rewarded to the player for participating in this content, and not rewarded to the player for not participating in the content. There are a lot of things in this game, and other games, that are rewarded by participating. As mentioned, I do not participate in the content of building multiple bases by default. So how does this new information and new content affect me? Currently, it makes me want to try my hand at building multiple bases. The worst thing that happens if I opt out of doing that, is the game plays exactly the same as it does before this update. It's not like I have to watch everyone else in my world gain an advantage because they're participating in content that I am not. The world I play on, if the participants choose to have one big central base, will play exactly the same as it did before this update, save for the "penalty" of increased prices. My last playthrough I had enough money to buy every single item as it became available from every single NPC that I unlocked, as they arrived, with tons of money leftover by the time I finished the actual progression of the game, wherein I could then buy all of the extremely optional high-expense items for the sheer sake of collecting them at my leisure. Dang, I really gotta break that habit of passive aggressively suggesting that it's extremely easy as it is to make money in Terraria and that the imposed penalty that has probably been thoroughly tested by at least a dozen dedicated testers has probably been deemed completely fair, several of whom probably have the proclivity of making massive central super-bases anyway.
So, what are the obvious downsides? Of course, the trade penalty. Of course, the pylon penalty. Of course, the not-having-a-centralized-base penalty. Is the trade penalty such a deal breaker in the sense that money is so important to some players that even a marginal tax is enough to completely cripple the player's economy, but not enough of a deal breaker that the player has to make settlements in order to circumvent the trade penalty when money is so clearly a driving force in the game? I don't know, that's not a question for me to answer. The pylon penalty. Does the requirement of building multiple settlements in order to institute a rapid transit system between the settlements outweigh the actual benefits of having all of your NPCs easily accessible in one super-base despite the fact that most of the NPCs are most assuredly not being used on a day-to-day basis as it is, especially later on in the game when certain NPCs become redundant if not completely invalidated? I don't know, not really a question for me to answer. I think the real problem here, that a lot of people might not be willing to admit...is that it's a change. A lot of people see it as an attack on their playstyle. In actuality, it's the encouragement of other playstyles. Yes, I'm aware that some people will argue that it's a discouragement of their playstyle. Yeah, I guess you have a point? But if the prices/costs were nerfed/increased across the board, without it being tied to the actual happiness of NPCs, and the only thing that existed were the bonuses for making NPCs happy and the penalty for unhappy NPCs didn't exist, I feel like people wouldn't be as mad...despite the fact that it would be the exact same in the long run.
Why shouldn't the dryad be happier in the jungle, the shroomlord be happier in glowing mushroom biome, the fisher be happier in near the ocean? Why shouldn't there be bonuses associated with that. People have been asking for that for awhile, to have better benefits for exactly that. As easy as it is to make money in this game, the update is probably going to make it even easier to get money. I don't consider it a discouragement of the systems that have been in place for years; I consider it a slight nerf to money usage, which can be completely negated by NPC happiness (and we don't even know how easily it will be negated at stage 1, btw...I predict pretty easily.)
I for one am excited. I exist exactly in the demographic that is most heavily impacted by these changes, and yet...I see them as utterly inconsequential and I will gladly try my hand at building multiple bases. I see them as settlements and my reward for said settlements and thinking about which NPCs should live together and how to make them happy will be enhanced and speedy travel across the map, not that there's any dearth of ways to quickly get around the map in this game. And if that fails for whatever reason, I will still have a super base rigged up in the center of the map, I will still have my queen and king statues, and then I'll just see about making artificial biomes attached to my base and see how they deal with that. In the grand scheme of things, I don't even remotely consider it a deal breaker. I understand people's frustrations, I understand that people feel insulted, slighted, annoyed at the changes, I simply do not share any of the sentiments, and I definitely don't see it as a change that's going to be relevant in the long run of my next playthrough. That's just my opinion and analysis of these minor changes. And yes, I do entirely consider them minor.
But I didn't pick a side.