I've been doing some regulating lately, with similar cars.
Firstly, some cars have been butchered by PD, plain and simple. These cars will never pair up properly with others, they must be identified and avoided for any PP tests done. The Eneos SC430 and Woodone Advan Clarion GTR both have what seem to be "tire penalties". What it means is through no amount of regulation to faster cars can these cars reasonably compete with the rest.
PD given natural tendencies are the best thing any car can get for good performance at any given PP. Prime example is the GTR SuperGT cars, which are now the slowest in the regulation, not in top speed, but acceleration. But they're still on par over the course of most tracks, the fastest on some tracks even, all with one of the lowest PP ratings.
Powerband's will destroy a PP rating, for example, the Xanavi Nismo Z is running on par with the GTR's, 616PP for the Z, 607PP for the GTR.
NSX's have good power and speed, along with handling...sort of. They can't corner nearly as fast as the GTR's and SC430's, but at the same power, they are faster in a straight line. We ended up having to add 30kg's to the good handling cars, and still had to use extra speed to make the poor handling cars keep up over the course of the season.
Cars with better cornering still corner better, and are a bit quicker around tight tracks, and the less cornering endowed cars are a bit faster on high-speed tracks.
The YMS Supra stands out at only 604PP, likely due to it 53/47 weight balance. PD does not recognize 50/50 weight distribution as optimal, but rather the more you throw on the back, the better they believe your car will drive.
So IMO, the natural programming by PD is the greatest PP marker any car can have.
Over 600, Aero starts playing a much more significant role, and very quickly tops the list, it's also dependent on tires.
It's also tough to decipher which hurts more, between powerband and weight.