I remember reading a while back that there is actually such thing as engine damage in the game. Not chassis flex or dirty oil, but apparently you can actually cause permanent (if minor) damage to the engine if you over-rev too much. I remember someone testing it with the Team Oreca Viper - they compared a brand new one to one that had sat with the engine bouncing off the rev limiter for several minutes, and I think there was a difference.
Yes there was such a test. The permanent power drop that comes from use was apparently shown to be accelerated by over revving. However, the results of this were obvious from the power figures. If all these cars are showing the same power, then this is not the problem.
Remember though that there are a number of places in GT4 where you can see the car's power. Are all the cars showing the same power figure whereever it is shown, or are the figures the same at race start but, say, different in the setup screen or in the garage?
I suspect some kind of tyre bug. If this is so, it should be possible to match one type of tyre to a different type type on one of the other cars by checking lap times or acceleration runs (acceleration runs with TCS on to eliminate errors through loss of traction). If the superAudi on N1s performs (and, importantly, feels the same around a track) as the other Audis on, say, N3s or S1s, then the car has a tyre bug. Also, if it's tyres, can't you feel the difference on a track? The blue one would feel much better in the bends if it thinks it is on superior tyres. If it's power then the blue one will feel a bit better on the straights but will feel no better when cornering as it would run out of grip at the same time as the other cars. In fact, if the power increase is enough to give a second and a half per lap, then the car may feel slightly worse in corners as entry speeds will be higher and the throttle would be more sensitive.
If it has extra power this might be checked on the Test Track. If it has more power it will have a higher top speed - if it does not run out of revs in top gear. I don't think tyres have any effect on top speed, only on acceleration and braking.
Finally, my Alfa GTA felt much quicker in acceleration, braking, and throttle response, and was therefore more agile in bends, when I installed a racing clutch and flywheel, and carbon propshaft. This gave me nearly 2 seconds a lap around Tsukuba with no other mods, on N2 tyres, which is a substantial difference. These mods do not affect quoted power or weight figures, if memory serves, but will be obvious when driving from the faster gear changes.