I (sigh) agree with the NYT. They are horrible for living in.
They lose a bunch of strength when you cut doors and windows in them, they take more work to make nice than just building a nice place, and my experience has been they get rust holes in them by about 10 years of use.
They are designed to be semi disposable in their intended use. Not something you want to build a house with.
This has been my experience. By the time you make the container nice, you're better off just building something of the container's dimensions directly. Or dimensions that are designed for human habitation as opposed to shipping.
You'll get something that is cheaper, more inhabitable, and lasts longer.
That isn't to say that I'm opposed to any other type of factory built housing - trailer homes, manufactured, modular, whatever. Each has their place. Even container homes have their place, I just don't think they have a place beyond the niche they're currently in.