Is it permissible for me to pray alone if my father prays Shafa' and Witr with the Fajr Adhan and recites Qunut supplication during the obligatory Dawn prayer?

Do not abandon praying with your father merely because he does not pray Witr with you, or does not perform Qunut in Witr, or performs Qunut in Fajr. This is because Qunut in Witr is not obligatory and is permissible, and Qunut in Fajr is recommended according to some scholars. If your father delays Witr until Fajr, then it is sunnah not to delay it, and he can be advised gently and reminded of the hadith.