The 2012 regs stipulated that the driver had no control over when the hybrid system came in, it had to be done through the throttle pedal only. It's up to the teams to map that with the TC to provide the best acceleration and consistent throttle response. If you had the hybrid go to the rear wheels, as Toyota did, then you can use it at any speed. It was only Audi with their FWD hybrid deployment that had to be over 120 km/h before they could use it. I don't know how Toyota had theirs work on the real car, but the way it deploys on the GT6 version is somewhat realistic just comparing it to how the rear car accelerated out of slow corners. The way it charges isn't right still, as it seems to be the amount of time you brake for, not how hard you brake. You can have 1% brake pressure and still charge the hybrid system as quick as 100%.
Try comparing lap times at Spa or Silverstone, you'll find on RM tyres they're close to real life. I'd assume Fuji will be the same. The GT6 version of Le Mans is far too uneven in places and it really makes the car hard to drive, the track isn't anywhere near as bumpy as it used to be, as they did a lot of resurfacing.