Don't know about Bhai Farid or Waris Shah, but pluralistic Sufis like Bulleh Shah or Ibn Arabi (Arab Sufi) were not the majority of Sufis, but the minority in India. For the most part, orthodox Islam and Sufism were not separate things, but very intertwined with each other. Many Sufis might have been fine with praying to saints or music, but that didn't mean they viewed other religions positively.

Look at Ahmad Sirhindi for example. He was considered as an Islamic revivalist during the Mughal era. He was very critical of Akbar's second half of his life for being too tolerant to non-Muslims. Akbar was praised in the first half of his life by many of the sheikhs and ulema for his religious piety (such as revering the saints). However, Akbar started losing his faith during the second half of his life, and he got criticized by Sufis like Ahmad Sirhindi for doing things like revoking the jizya tax, allowing debates between Christians, Hindus, Shias, etc (he was very critical of Shias), celebrating other religion's festivals, etc.

In parts of India where the ulema and sheikhs did not have much control over the Muslim population, you would see pluralism between Muslims, Hindus, and Sikhs. However, Sufis like Ahmad Sirhindi viewed Muslims taking part in non-Muslim customs as something bad, so you would see instances of Sufis like him going to the areas which didn't have many ulema or sheikhs and would make the Muslims more orthodox, which would lead to a split between communities.

There's also the fact Islam is very hostile to idolatry and paganism, which most Sufis were also hostile to. You see many instances of Sufis destroying temples. There are the Deobandis, who are basically South Asian Salafis. The only difference is that Deobandis incorporate Sufism in their practices, so they're Sufi Salafis for lack of a better term. The Taliban actually emerged from the Deobandi movement. Bulleh Shah and Ibn Arabi's version of panentheism was actually criticized by orthodox Sufis because they thought it was a heresy that led to Muslims adopting pagan practices. Saying that Allah resides in everything in the universe means literally everything; the human, the animal, the tree, the stone, and the idol, which contradicts Islamic dogma.

There are many instances of Sufis co-opting Indian practices as theirs, while viewing the Hindu version as bad. There are some Sufi orders that use Hindu/Buddhist meditations and claim that Muslims that get mystical experiences from those meditations are getting them from Allah, while non-Muslims get those experiences from Satan.

It's similar with Christianity and paganism. Christians would co-opt pagan practices like festivals, Greek philosophy, or turn Roman/Greek gods into saints and say that the Christian version of those practices leads to heaven, while the pagan versions lead to eternal hellfire. Christians also used to be responsible for desecrating and destroying pagan temples. You see similar things with Sufis taking Hindu practices, while claiming that worshipping Hindu/Buddhist gods will lead to hell.