As I understand the story and I'm doing this from memory, so I might not be completely accurate:
First of all, officially there are no 330GTO's. The O stands for 'omologato', homologated. This means that the story that Enzo told the officials was that they were improved versions of the 250 SWB - basically the same car with an aerodynamic body. As we all know now, Enzo lied a bit. He also lied about building 100 of them - this is why the chassis numbers of the GTOs are so far apart.
Anyway - to be a GTO, it had to have the engine capacity of the 250 SWB. So the 330's did not qualify. They raced in the Prototype class, not the GT class.
There are 3 "GTO's" with a 330 engine. All have the suffix SA in their chassisnumber (I think a reference to Superamerica, although I have no idea why - maybe a link to the other 4 litre car, the 400 Superamerica but that had a completely different engine), the 250GTO's have the suffix GT like all the road cars.
All the 330 cars have a similar body, which looks like the 1962 GTO body but with (I think all of them) a higher cowl for covering the carbs.
Performance-wise, I do not think there was a difference back in the time, or if there was, there is no way of telling now.
I'd be pleased if any more knowledgeable people on the GTO can correct any inaccuracies in the above (krasnavian?).
Yes, you are partially correct, the 330 "GTO" name never existed officially. Until 1961, sports racing cars where limited to 3 liters. For 1962, in a attempt to open those sports car championships to a bigger manufacturers base the FIA announced that the constructors Championship would be run for grand touring cars. Although sport prototypes would still be allowed to compete to add spectators appeal, but all championship points would go to the GT class.
At the time therefore, Enzo Ferrari was concerned that there would be new competitors in the prototype class for overall victories, and in the grand touring class for world championship points. Freed from the 3 litre limit he began a series of experiments with four liter engines.
Because of the bodywork, it is often described as a 4 litre GTO. The chassis actually is a 539 250 GTO 2400mm chassis, (3765SA) whereas later cars have partially a 400 SA chassis with different tube size, diameters and front cross member (Superamerica, hence you are right again). The engine fitted to it is a tuned version of a 400 SA enginetype 163 LM (!). So engine and chassis mostly = Superamerica, body = 250 GTO (almost)
But the story does not ends here, after all that is said the history of some of these very rare cars become totally diversified as the type 163 400SA engine block proved too short in its dimensions limiting any bore increase. Also it had a tendency to overheat if pushed too far and led fastly into the redevelopment of a larger block which then first arrived in a 250 P chassis in 1964 as a 4.4 liter CanAm motor. Also some of those engines where mounted in different chassis with different wheelbase lenghts (2400/2450/2500mm).
Interesting these cars and stories. There is much much more to be said about and all those 6 different chassis numbers of the type (3765SA, 4381SA, 4453SA 4561SA, 4619SA and finally 4725SA) all have their very own histories and specifications...chassis, engine and body wise. (Information partially from Cavallino articles from the time)