Because of their intended purpose. Everything from the Sauber C11 to the TS050 were prototypes. But the CLK LM and F1 GTR were both homologated sports cars. The LMH category was intended to be homologated but that reg was gotten rid of at some point.
But if we're going by lap time, the TS050 was a whole ten seconds faster than the GR010. The 2011 R18 was a dog - diesel, non-hybrid, rwd, six seconds slower than the Peugeot 908. It ran a 3:25 compared to the Peugeot's 3:19 and the TS050's 3:17.
That is not correct, except the part that, at some point, the Hypercar category was suppos d to be homologation vehicles.
The R18 wasn't 6 seconds slower than the 908, In fact they lock down the front row. You can't compare lap times from 2010 to 2011, because there was a major regulation overhaul, with the engine sizes being heavily reduced, on case of the Audi and the Peugeot, from 5.5 l to 3.7, in order to reduce overall speeds.
It's precisely like comparing times from TS050 with the GR10, both cases regulations were established to reduce laptimes to a target time several seconds slower than previous generation.