The rules are pretty black and white with how cars are homologated. It had to do with their ECU fuel maps - so they have a fuel map for safety car pacing, a map for regular racing, and a map for qualifying. Those are carefully spec'd when a car is approved for homologation. I don't think anyone knows exactly what the fuel mapping did or how exactly it affected it, but either way, there's pre-determined rules they have to adhere to and it was obvious they didn't run something that was approved.
It was a very harsh penalty but I think it was black and white. The marshals told them for the penalty though Noel that if they served it under caution they'd serve longer.