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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!
Quite. So are such deviations on compulsory bits considered insignificant/minor/ moderate/ severe? or what's the usual penalty might be a better question?