Physical attacks and soul attacks were two completely different attacks. Physical attacks, as its name suggested, would leave physical injuries and could be countered with strength. Soul attacks, on the other hand, left no injuries on the physical body as it would destroy one's soul. Moreover, it was almost impossible to stop it unless one had an object with a Restriction Formation. Unfortunately, Restriction Formations were only available in Devata Realms.
For this reason, Gongsun Wen Tian was confident the defective metal piece that Duan Ling Tian had shot out would be helpless to stop his soul attack. He was certain his soul attack would easily pierce through the defective metal piece and destroy Duan Ling Tian's soul!
Similarly, Gongsun Hong who was standing next to Gongsun Wen Tian and Xuan Yuan Zhi, the Nine Tribulation Bodiless Celestial from the Yellow Thearch Mansion, who was standing next to Duan Ling Tian, had the same thought as Gongsun Wen Tian.