I think you have a few things confused with regards to realism. Firstly it is the Ford GT not the GT40 which is in Gran Turismo.
With this in mind, its worth considering a few things.
Suzuka is a technical handling track, your speed through the corners makes such a difference in lap times. The elise is a small lightweight car built with lapping a track quickly in mind. The GT is an expensive super car with luxuries, power and having a high top speed in mind. While the GT out accelerate the the tuned elise (despite its higher weight) and will generally go much quicker down a straight its not anywhere near as quick through the corners, it may be wide and have chunky tires but is far heavier and carries little in the way of aerodynamic assistance i.e rear wings for downforce. The Lotus which was already feather weight to begin with with the help of a big rear wing and splitters flies round corners at much greater speed than the ford GT. This means the Tuned elise is much quicker through the esses than the ford GT. The ford GT is quicker through the second part of the track due to much more power on the long straights but it isn't sufficient to make up the time lost against the tuned elise in the esses on the first part of the lap.
I hope that clears a few things up.
