Thats definately not true. Did you ever build a neck-through? It is definately more difficult than a bolt-on. I am not the only one with that opinion. In the book "Build Your Guitar" the author confirms that theory. If you have a jointer and a planer, then it is not much more difficult than a bolt-on, but without these tools it is very difficult to plane the wings and the necks 100% perpendicular and even. Another thing which makes the neck-through much more difficult is the fact that you cannot allow to mess something up. If you mess up the neck, then you have to throw away the whole thing. With a bolt-on you can build the neck and the body seperately and if you mess one up you can simple start over with the part in question and do not have to build a new guitar. Additionaly the handling of the neck-through during building, finishing and fretting is much more difficult, because you always have to deal with the whole guitar.
Just my opinion though....feel free to flame me....