I think it's a little of both the updated physics and updated skills, but sometimes you just have bad days, or impatient days. Improvement is always possible, and it's always a good thing. When you watch the Stig go around the Top Gear track, do you ever wonder if that's truly the best time those cars are capable of? It might be the best time he got that day, but maybe if he tried again the next day and pushed a bit harder, or the next week or month, he'd do better.
The real NSX-R at Suzuka ran a 2:34.0 while GT6 version ran a 2:19.6 for a difference of 14.4 seconds.
At 284 hp and with CM tires, I was able to get a 2:28 which is still 5 seconds faster than reality, and on CH tires I could manage a 2:34 which almost exactly matches the real-life time.
However, the real NSX could probably knock off 2 or 3 seconds with more laps, as I can see a lot of room for improvement in a few of the corners, and there was a missed shift.
And here's an EK Civic Type R with a time of 2:49.1 compared to my 2:33.5 for a difference of 15.6 seconds! Again, under 2:45 is probable.
With the '98 Civic Type R, on CM tires, I could manage a 2:42 which is 7 seconds faster than reality.
It seems like something between CH and CM tires would be the most realistic, but that doesn't make logical sense.