To a certain extent, you can make this point about almost any change. Any major change in a game will favor some play styles over others, and that is what is happening here.
You can still make shoeboxes, the NPCs will still live in them, and you can still trade with them, you just get worse trades. This doesn't really affect your ability to play the game. I find I get way too much money anyway.
Even if you don't want to get penalized. It isn't that hard to make the NPCs happy, just put a pylon in their preferred biome, and build a slightly larger shoebox next to it. I think this would be a net positive since you get to teleport using the pylons, which you wouldn't be able to do if you didn't put the NPCs next to them. I don't think this is any inconvenience.
Edit: On top of this, the base-building aspect of the game has been there since the very beginning, or at least for a long time (I only started playing in 1.2), the happiness system doesn't force you to build nice houses, you can still build pretty much the same houses you could before. You just need to make them slightly larger and spread them out a bit. I'd hardly consider this forcing the players into base-building any more than the original system.