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It's a matter of choice. You can set the potential energy to be any value at any angle. You don't even have to have a zero-value at all; you could make $U$ purely positive or purely negative if you're feeling adventurous. But the advantage for $U(\pi/2)=0$ is, as you said, the simple expression $U(\theta)=-pE\cos\theta = -\vec p \cdot \vec E$ instead of ...

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