Playing devil's advocate here.
Winterkorn prefers a centralized management style, where everyone report to someone then at last reports to him, kind of like the old communist party style.
Piech on the other hand is a more hands on guy, he wants to put his fingers on everything and anything.
The coding of software starts at a lower level. That guy reports to the engine manager that the engines won't pass. Would he reports up the chain and raise losing his job because the company dumped a lot of money into the engine and 'his' project failed? Maybe hide that fact when he reports upwards while ordering the coders to cheat the test cycle.
From this perspective Winterkorn would have never know. Piech on the other hand would. Maybe he knew all along, yet didn't say anything, or even approved the practice.
He dropped the bomb shell on a board meeting, Winterkorn said we can't do that, but Piech say keep on cheating. Piech wants to remove Winterkorn as a result. But the board ended up siding with Winterkorn and remove Piech instead.
Meanwhile, they try to see and find a solution quietly. Didn't happened.
Piech is a ruthless man, it is not unimaginable that he won't try to cheat to get to the top. Hell he cheated on his cousin already with the affair and then try to maneuver the share holdings to gain control of the Porsche empire.
Most of you assume Piech is always the good guy simply because he carries the bloodline of the Porsche family, but every family gene pool will have their shares of bad apples.
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