It's a tricky subject. Theoretically, BOP could be ignored - just publish fastest times from all series and whichever series happens to have least restrictive BOP gets the honors of showing the fastest lap time for that particular GT3 car.
But there is still problem of defining models for those GT3 cars. One way would be to just add one page per model name (458 GT3, 488 GT3, 997 GT3, 991 GT3 etc), disregarding any changes that may happen from one year to another. In MotoGP there is similar situation - for example, Yamaha M1 is called "M1" for several years, even though there are myriad of changes. Yet I have added just one page: http://fastestlaps.com/models/yamaha-yzr-m1