Is performing the Witr prayer as three rak'ahs, raising the hands for the takbir before Du'a al-Qunut, considered a correct way to make it different from the Maghrib prayer?

The Prophet's (peace and blessings be upon him) prohibition of performing Witr prayer with three rak'ahs does not mean raising the hands for the takbir before dua' al-qunut. Rather, it is a prohibition of sitting for the first tashahhud so that it would resemble the Maghrib prayer. Raising the hands is only prescribed in four instances: the takbirat al-ihram (opening takbir), bowing (ruk'u), rising from bowing, and standing up from the first tashahhud.