I'm thinking one way to easily do motor doping is via the bike changes. A rider swaps a doped bike brought in by the team that wasn't checked at the start during the easy portions and rides 100km saving watts along the way. They then change back to a regular bike before things get intense and meanwhile the team finds a way to discreetly get rid of the doped bike.
After the stage the doping controls check the regular bike, but are unaware of the existence of the doped bike.
After the stage the doping controls check the regular bike, but are unaware of the existence of the doped bike.