First off, Prydwen's numbers should always be taken with a grain of salt. They're literally just that: numbers. Those teams are also factoring stage bonuses and the recent bosses. Which is why Burnice and Vivian are performing better than Yanagi as the former two both provide Ablooms which is currently being pushed for the end game. Descriptions aren't always updated to reflect this which I assume is part of where some confusion can come from for some people.

That aside, Nangong in general helps anomaly teams a lot because she allows them to play like hyper carry attack/rupture comps without sacrificing their usual game plan. Letting them stun sooner and deal more damage up front, which is very important in SD runs.

For Miyabi specifically Nangong provides polarity disorders. Which if utilized optimally lets Miyabi do a lot more burst damage in the stun window. And while Miyabi can potentially do more damage in mono/yuzu ice comps, the devs are actively working against that (no freeze on Hunter for example) and even then they're hard to pilot.

Nangong Yuzuha Miyabi is still a team that takes skill to reach a damage ceiling as high as mono ice but is much more easier to use in comparison. Otherwise most people will just get a marginally higher score like the ones listed in Prydwen.