The two instruments are different, but not as different as some may claim. As the article points out, the Flutophone can play the full chromatic scale, just like a recorder, and not be stuck in the key of C, as some sites have claimed.
If the recorder is a real woodwind instrument, with a real reed, it should produce a richer sound than the Flutophone, especially if the body is also made of wood. However, its use and care (and initial expense) might not make it the ideal instrument with which to introduce a young child to the joys of music making.
However, most of the recorders I have seen in elementary school bands were only made of plastic colored to resemble wood. If they use plastic reeds as well, then the only difference between the two instruments is their lower diameters, which would have little effect on how they are played and how they would sound.