I believe Pyrefly is stricter, so it may be a better choice for new projects but harder to integrate into existing ones without type-checking.
Pyrefly spits put around 200 errors for the same codebase.
Most errors are related to SQLAlchemy.
Perhaps you should do the upgrade (https://docs.sqlalchemy.org/en/20/changelog/whatsnew_20.html...) and try again?