Seems a little idiotic? Building the 5th largest ship seems much better...you get much of the scale benefit without having to worry about all the possible issues with harbours etc.
Since this ship was able to dock at Langelinie in Copenhagen (which quite frankly, isn't the most adaptive harbour in the world), I am pretty sure harbours like Rotterdam and whatnot can handle it.
Sure, it cannot sail through the Panama Canal, but as mentioned in the article, it is for the Europe-Asia route, which tends to go south around Africa anyway. Because the Suez canal wouldn't be able to handle the 5th largest ship in the world anyway.
Edit: It turns out I am wrong, they can actually use the Suez Canal (even the Triple E mentioned in the article).
However, unlike the Triple E (of which 20 are to be built), the Seawise Giant was a one-off.