Should he pray behind those who pray Witr with three rak’ahs and two tashahhuds and one salam, and they recite qunoot before bowing?

Firstly: 

What the imam and the worshippers did, praying Witr with three rak’ahs, two tashahhuds and one salam, and reciting qunoot before bowing, are issues concerning which there is a well-known scholarly difference of opinion between the Hanafis and the majority of scholars. There is something makrooh about praying Witr in this manner. Praying Witr with three rak’ahs may be done in two ways, both of which are Islamically acceptable. They are as follows: 

1 – Praying the three rak’ahs one after another, with one tashahhud and one tasleem.

2 – Praying two rak’ahs then saying the salam, then praying one rak’ah on its own. 

You will find a detailed discussion of both ways, along with the evidence for them, in the answer to question no. 46544. 

As for praying three rak’ahs with two tashahhuds and one salam, it is narrated that this is not allowed and at the very least it is makrooh. We have quoted the fatwas of scholars forbidding this in the answers to questions no. 72246 and 26844. 

With regard to reciting qunoot before bowing, there is evidence for this in the saheeh Sunnah. Those who say that qunoot should be recited after bowing also have evidence. There is no reason for denouncing, let alone disputing, let alone doing what is worse than that, namely refusing to pray behind that imam. 

The issue of qunoot in Witr has been discussed in the answer to question no. 14093. 

Secondly: 

There is nothing wrong with praying behind them, even if they pray in the manner that you have described, because what they are doing is following a mujtahid imam, so there is no justification for refusing to pray behind them or causing division amongst them, especially since you are living in a kaafir land and whatever troubles arise among you will reflect badly on Islam. 

Shaykh al-Islam Ibn Taymiyah (may Allah have mercy on him) said: 

The scholars differed concerning a situation where the imam does not do what the person praying behind him believes to be obligatory, such as not reciting the Basmalah when the person praying behind him believes that this is obligatory, or he has touched his private part without doing wudoo’ afterwards, when the person praying behind him believes wudoo’ to be obligatory in that case, or he prays wearing the skins of dead animals that have been tanned, when the person praying behind him thinks that tanning does not purify, or he has been treated by means of cupping and did not do wudoo’ afterwards, and the person praying behind him thinks that wudoo’ must be done after cupping. The definitively correct view is that the prayer of the one praying behind the imam is valid even if the imam follows the wrong view with regard to a disputed issue, because it is proven in al-Saheeh that the Prophet (peace and blessings of Allah be upon him) said: “They lead in you in prayer, and if they do right, it is for you and for them, and if they do wrong, it is for you and against them.” 

Similarly, if the worshipper follows an imam who does qunoot in Fajr or Witr, he should pray qunoot with him, whether that is before bowing or after, and if he does not do qunoot, he should not do qunoot with him. If the imam thinks that it is mustahabb to do a certain thing in prayer but the one who is praying behind him does not think that is the case and he (the imam) decides not to do it for the sake of harmony and unity, that is better. 

An example of that is Witr, concerning which there are three views among the scholars: 

1 – That it should be three rak’ahs one after another, like Maghrib, as was the view of some of the people of Iraq.

2 – That it should only be one rak’ah performed separately from whatever comes before, as was the view of some of the people of the Hijaz.

3 – That both are permissible, as is the apparent view of al-Shaafa’i, Ahmad and others. This is correct view, although they preferred that it should be done separately from whatever came before. 

If the imam thinks that it should be done separately, and the congregation thinks that Witr should be done like Maghrib, and he agrees to do that so as to create harmony, that is better, as the Prophet (peace and blessings of Allah be upon him) said to ‘Aa’ishah: “Were it not that your people have only recently left Jaahiliyyah behind, I would have razed the Ka’bah to the ground and rebuilt it with two doors, one through which the people might enter and one through which they might exit.” But he decided not to do that which was better, lest it put the people off. End quote. 

Al-Fatawa al-Kubra, 2/476 

And Allah knows best.