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That's not a conspiracy at all.
Whipple pays Ford for the ability to sell a tune for their ECU to go with their supercharger kits. Whipple is able to bring their product to market months or years before a crack or work around is figured out for other brands. This isn't just them, I'm sure many other companies license thile same way, and the OEMs likely require them to put some sort of indication that they had once tuned the vehicle in for warranty purposes.
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