Yeah... after being around long enough seeing Japanese products, you learn quickly that even "official" products often can't seem to pick a romanization and stick with it. I wouldn't place too much faith in anything that doesn't come directly out of the artist's mouth... and even then, the artists aren't always known for picking romanizations that would seem obvious to English-speakers.
As for everybody above who insists that they will always call him "GO-dot" (like "robot")... you remind me of a young me. When I was 13 years old, I swore up and down that there was a character in Ranma 1/2 named "Rye-oh-guh" (Ryoga). Even after being corrected by a person who had recently graduated college with a degree in Japanese that it was called "ReeOH-ga".
Now, however, I've learned that when there is a "right" pronunciation, there IS a "right" pronunciation. There's no point in being stubborn in what *you* think "sounds better". "Godot" isn't one of those words that has more than one right way to say it (e.g. tomato, or differences in American and British English.) When I learned that intentionally mispronouncing something out of stubbornness does nothing more than display my own ignorance to people who know better, I stopped.
Honestly, everybody is free to do as they wish, of course, and if people want to call New York "Naw Yirk" because they think it sounds cooler, it's their prerogative. Alternately, if they insist on loudly pronouncing the "p" at the beginning of the word "phrase", because hey, that's how it's spelled, they're welcome to do that also. Just know that it's considered stubborn ignorance for the most part, moreso than voicing a preference. I know, because I've been the stubborn one before.
EDIT: Of course, that doesn't mean you have to pretend you're Japanese, or even French, when you say it. No need to be the newscaster pronouncing "Guatemala" in the perfect Spanish accent (WATEMALA or something). I don't know how to properly pronounce French any more than the next guy, but I believe the accepted pronunciation in English of the the French name "Godot" is "guhDOUGH" thereabouts. That's not hard to pronounce by any means.
(HOWEVER. According to this site, the accepted American pronunciation is not correct either. Funny how that works, isn't it? Beckett says to emphasize the first syllable (GOdough)... however it's far too late to tell that to Capcom, the Japanese creators of the game seemingly tried to emulate the American pronunciation, according to the kana. *sigh* What tangled webs we weave.)
And it sounded like my younger brother's nickname no less. 