While this is true, diesels often come from the factory with a conservative one size fits all engine tune.

You can usually make the car more fuel efficient and/or add a bit more power if you do it properly. Potentially you can even make it more reliable. One of the things manufacturers caught up in dieselgate did, is recall cars and give the engine a less polluting engine tune.

Obviously, that's not what most people do. They tune it to have as much power as possible (or if they're idiots roal coal) and are then surprised when the transmission or engine gives out prematurely, and the manufacturer no longer feels the need to honour the warranty.

You know how people say that a new car loses depreciates up to 20% just driving it off the car lot? Stuff like engine tuning is one of the reasons that difference exists. You don't know if the previous owner did stupid shit to the car.