The F1 GTR with the BMW Schnitzer is faster than the F1 GTR with the Kokusai Kaihatsu Racing livery in both the game and IRL, by a considerable margin, which is to be expected.
In terms of just the game itself, the BoP ruins the Gr. 3 F1 GTR, because without BoP, it is actually one of the fastest Gr.3 car in the game, if not the fastest, but it's handling is not as smooth as the other Gr.3 cars.
The Gr.2 F1 GTR is faster than the 2008 GT500 cars but slower than the CLK-LM and the 2016 GT500 cars. With BoP, the Gr.2 F1 GTR is arguably the slowest car of the Gr.2 class.
This is just one of the issues with having cars in the same Fictional Class when they are simply completely different. In the same way you can NEVER have a good BoP with LMP1 cars and Gr.C cars, you are definitely not going to find a good BoP with 90's GT1 cars and late 2000s GT500 cars. They all have vastly different philosophies... In fact, the GT500 cars are basically GT cars with lots of Aero bits while the GT1s are pretty much full blown prototypes.
Gr.3 and Gr.4 can find balance because the cars are all based on road going versions which helps, but even then you have a few oddballs (Veyron Gr.4 for example, either being terrible or the best thing ever). They are also based on very similar set of regulations (GT3, GTE, GT4).