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Not doing the designated parcours is considered serious. He'd definitely get a penalty if they believed he hadn't done it. Generally the penalties are pretty light - maybe a couple of hours if it wasn't a major short cut.
Off topic rant on penalties:
When I did it I felt that the penalties were generally too light to offset the benefit that people got from using illegal roads. eg I rode down a rough road in Macedonia while some people went on the parallel road which was a motorway. They got penalised by 2 hours. In truth they probably saved more time than that, maybe 3-4 hours. But because they saved the time it meant that they could finish a day earlier, so saved a night's sleep as well - so the benefit was more like 8-10 hours for a 2 hour penalty!
That's why you need to have your tracker set to update ideally every 5 min. @hippy had his only updating every half an hour which isn't enough to give your dot-watcher a reliable record of where you have been in the mountains. He's now changed it to 10 mins which should be better, but still not ideal. Most riders have it on 5 min updates.