Sect Armaments were something condensed from a massive amount of Fate, and it was very similar to a Nation Armament. However, it was also quite different – Nation Armaments required a King's Fate to control, while Sect Armaments required a Sect's Fate and a Sect's acknowledgment. As such, ordinarily, only Sect Masters could use them.
Moreover, their attributes were different as well; Nation Armaments had a Nation's power, while Sect Armaments had a Sect's power.
Neither was weaker than the other; often, Sects were as powerful as nations, but they were simply run as Sects.
What Zhao Fu was concerned about was whether this Sect Armament could be refined by Great Qin. After all, Great Qin had only refined Nation Armaments and had not encountered Sect Armaments before, so Zhao Fu had no idea if Great Qin could refine Sect Armaments.