I think if you go back and watch all the ALMS races this year, you will see a perfect example of cars, the Audi R10 and the Porsche Spyder, that are very different yet run nearly the same lap times. One is an LMP1 and is larger, longer wheel base, with gobs more power... but it is heavier. The LMP2 Spyder is lighter, smaller and much more nimble.
On the tighter tracks, the Spyder was the clearly faster car. On long tracks, the R10 was clearly faster. But on the in-between tracks, it was a heck of a battle. If the R10 ever got in front, it was very tough for the Spyder to pass because the R10 would just gap them on the straights.
But if the Spyder could get by in the corners, and they had enough time before a straight, they would pull away.
On tighter tracks, the R10 would use traffic to their advantage because of their huge torque and make quick work of slower cars. The Spyder would lose momentum getting around traffic allowing the R10 to either catch up or build a gap.
It all made for some exciting racing.
The point is, even if all the GTR cars are made so that we can run identical lap times in hot laps, racing against each other will still be a challenge. For example, the XRR has a bit more top speed down the straights, but it is almost useless because the FXR will get a much, much better jump exiting the last corner. They can get so good of a jump, that the XRR can't catch up even along the longest straights. To get by, you have to race. Find the weakness in the other driver or other car, and fight your way past. That is as it should be.
So, don't worry too much about equal lap times. I think they should be as close as is feasibly possible. But, because of the different nature of each car model (thank you Scavier), there will still be advantages and disadvantages to each car. This is as it should be because they are different cars. It ain't spec racing here.