I too noticed the penalties at Le Mans, even in a race with a lot of fast guys 90% of the drivers ended up with a penalty at some point.
I think GT may be adopting the rule that Le Mans had a few years ago about the white line being the limit of the track, not the curbs. Meaning four wheels inside (or outside) the white line counting as a penalty. It was particularly noticable at the exit of the Dunlop chicane (running wide was a penalty) as well as the Mulsanne chicanes.