Sounds like Lexus want to encourage owners to buy a new car every 3 years!
Alternatively, Lexus cars are also more expensive to buy, and so presumably more expensive to fix under warranty. Perhaps 3 years it the point at which the cash reserve Lexus would have to put aside to cover warranty repairs, would make the price of the new cars too expensive, or they may be more complex and so more likely to go wrong.
The hybrid battery needs a longer warranty than 3 years or people would not buy a hybrid for fear of a big bill to replace them.