Let's be clear, in most situations in GT3 the GT-ONE is *slower* than the R390. In real life this would not be the case.
At Le Mans in 1998, these cars went head to head. You could say the R390 won, because they had finishers 3rd, 5th and 6th and Toyota only had 9th and 24th. But make no mistake, the GT-ONE was setting faster laptimes and was substantially more competitive. One of the GT-ONEs led with little over an hour remaining, but it broke down. The other cars were also competitive but were forced down the field by overheating problems etc. and finished quite low.
The GT-ONE should be the faster car, because it is in real life. But in GT3 it is not, for whatever reason. It has more power and you only have to look at it to see it is more aerodynamically advanced. However, it has a long wheelbase which makes it a real handful in slow corners. Also, in high speed corners, where it should excel, it is very edgy in comparison to the R390.
The R390 is a lot easier to drive. I'm a reasonably proficient GT3 player, and I got into an R390, which I had never driven before, upgraded to the max, put on super soft slicks and drove 40 laps at Laguna Seca. In the first few laps I struggled because it was new to me, but by the end, with a time of 1:00.621, I was 2 tenths slower than the R390-Laguna Seca lap record at GT3times. I have driven the GT-ONE for several hundred laps at various races but I was not within 2 seconds let alone 2 tenths.
At some tracks, like Midfield, the GT-ONE works like a dream and will easily beat anything except an F1 car. But at others, particularly SS11, it struggles, and the R390 is faster. Even the 787B (with 400 hp less due to lack of extreme turbo upgrades) can set faster times than the GT-ONE there because it is shorter, and has better agility in the slow corners.
Meanwhile, let's point out that without the silly arcade-like turbo upgrades in GT3, the 787B owns the GT-ONE and the R390.
To round things off, the R390 goes better in races than the GT-ONE and is easier on it's tyres. If you add in that it is usually slightly faster and handles better, you have an all-round better car.
I wouldn't be surprised if the balance of power has changed in GT4.