MY theory on the 488 GTB name....
My guess is that it is a reference to the 288 GTO which was the first "significant" turbocharged mid-engined Ferrari production model developed for world-wide consumption. It would not be hard to believe that Ferrari may want this car as the basis for the next "GTO" model, as then the title 488 GTO makes for an obvious reference to the past. In the same way that the 308 GTB begat the 288GTO, I think this could be their plan for this model. 488 GTO follows 488 GTB.
Perhaps they didn't change the name to reflect the displacement/cylinder count of the model as this car is clearly based on the 458. A move to a 398 nomenclature would be confusing step for most non-enthusiasts to keep up with and for people who don't know any better, the name 398 seems "inferior" to 458. Despite many of the company's model names reflecting the trend of naming the car after the displacement and cylinder count (348, 458, 288 etc.), most of the cars do not comply with that naming strategy anyhow (355, 360, 430, 599, etc.)
Just a guess.