In the name of Allah, The Most Gracious, The Most Merciful.
The type of witr in question which has three rak’ats, two tashahud and one taslim is from the math-hab of Abu Hanifa (may Allah have mercy on him), and according to him there is no correct witr besides this. He was however contradicted by the majority of scholars from the companions, tabi’een and those who came after them like Malik, Shafi and Ahmad. From the proofs used to deduce by Abu Hanifa is what was reported by Muhammad Ibn Ka’b al-Qardhi that The Messenger of Allah (peace be on him) forbade the offering of a prayer without full concentration. Likewise, what has been narrated from Abu Sa'eed that the Prophet (peace be upon him) prohibited the offering of a prayer without full concentration, and that a man should perform one rak'ah of Witr prayer. al-Nawawi graded the first hadith as weak in al-Khulasa saying: the hadith of Muhammad Ibn Ka’b al-Qardhi on prohibition of offering of a prayer without full concentration is weak and not attributed to the Prophet (peace be on him). Ibn Hazm said in Al-Muhalla (3/48): prohibition of offering of a prayer without full concentration cannot be authenticated on to the Prophet (peace be on him). Ibn Al-Qayim said in A’lam al-Muawiqeen (2/269): The chain of narrators of this hadith is not known; neither is its authenticity nor weakness and nothing about it is mentioned in the reliable books of hadith. If it was authentic its evidence would have supported what was held by Abu Hanifa. Ibn Al-Qayim (may Allah have mercy on him) said (2/269): Even, if the hadeeth was authentic, the term "broken prayer," is a description of a prayer whose rukoo' and sujood are not done well." In Fath al-Baari, ibn Hajar said, "The term "broken prayer" may mean a prayer where a single rak'at which is not preceded by anything is performed. Thus it is a more general than being just used to refer to Witr prayer made with or without salaam after two rak'ats.
Majority of scholars are of the opinion that it is permissible to perform three rak’ats of witr and a single taslim as indicated by the sunnah, and other scholars are of the opinion that it is detestable to pray three rak’ats of witr while sitting for tashahud on the second rak’at because it has a pattern of Maghrib prayer which is not permissible according to a hadith reported by Abu Haraira (may Allah be pleased with him) who said that The Messenger of Allah (peace be on him) said: “do not make three rak’ats witr which is similar to Maghrib, rather make witr of five or seven rak’ats.” [Narrated by Hakim and Ibn Hiban].
Al-Dar Qutni also narrated it and said: its chain of narrators is reliable.
With regards to the hadeeth al-Iraqi said, "Its chain of narrators is authentic." This prohibition is interpreted to mean preferring performing three raka'ts with two tashahuds. It could be interpreted to mean that the prohibition denotes detestability. In my opinion, the former is the preponderant opinion because the prohibition concerns the number. This is what is stated. What caused the prohibition to be interpreted as denoting detestability are the texts which were revealed and permit the other form of performing the Witr prayer. These are explicit texts or texts with an implied meaning.
However, what you mentioned regarding qunut before ruku’ is a broad issue. It was transmitted from the predecessors, among them the companions and tabi’een, likewise making takbir for making qunut before going for ruku’ was mentioned by Ibn Abi Shayba in his Muswannaf on the authority of Abdullah Ibn Mas’ud but there is weakness in its chain of narrators. It was disregarded by Malik in al-Mudawwana (1/192) saying: “a man makes qunut in the morning before ruku’ and does not make takbir for qunut.”
likewise Imam Shafi (may Allah have mercy on him) said in al-Umm: “this is an additional takbir in prayer which is not established neither by proof nor by analogy.”
What is apparent is that it is not permissible because the principle for acts of worship is that they should be based on textual evidence. However your question regarding continuing to pray behind people who pray witr the way you described bearing in mind that you follow Shafi math-hab and your desiring to pray behind the people of sunnah; you should know that Hanafites are from the people of sunnah and all praises are due to Allah. Even what was explained with respect to differences in opinion is a broad issue within the schools of thought. My opinion is that you should continue praying with them and follow them in what they will be doing, there is no harm in that, not only that but it is obligatory because this is what has been done by the predecessors from the companions and those who came after them, they used to follow the imam even they had differences in opinion even with respect to prayer itself in terms of its conditions and obligations. Ibn Qudamah said in al-Mughni (3/23): “if a person prays behind an Imam who prays three rak’ats witr with one taslim, he should follow the Imam so that he doesn’t contradict his Imam, and this was said by Malik too, in the narration of Abu Dawud, Ahmad said with regards to a person who makes Witr, and makes salam after two rak'ats, and the congregation forces him not to consider this salam but requires him to make three rak'ats, "If he does what they want and agrees to it, there is no problem."
Ahmad (may Allah have mercy on him) said a person prays behind an Imam who makes qunut in Fajr prayer should follow him and say Ameen when he supplicates. Shaykh al-Islam Ibn Taymiyya (may Allah have mercy on him) said in al-Ikhtiyarat (70): if an Imam does something justified by ijtihad (juristic deduction) he should be followed by congregants like in the case of qunut in Fajr or three rak’ats witr with one taslim, and someone who makes qunut should follow an Imam who does not make qunut if he prays behind him. In Fatawa al-Kubra (2/240-241), Shaykh al-Islam Ibn Taymiyyah responded to an issue similar to your question by saying: “what is correct is that if an Imam does something that is established by sunnah or prays witr in one of the ways mentioned in sunnah, then the congregants should follow him on that.”
And Allah knows best.
Dr. Khalid al-Muslih
18 / 09 / 1424 AH