I'm sure you're right that there are situations where mypy or ty or LSP give false positives/negatives, but in my use of them over the last ~6 months I really haven't run into many of those situations, or at least none come to mind. Libraries without type annotations do reduce the effectiveness to just what can be inferred by the type checker.
you need to work on big project for these flaws to become a problem. Say, you have a huge code base, 100000's of lines that you didn't write. Then you want to refactor a method's name. Python can't give you any guarantee the refactoring is fully complete. Only a real typed language can do that.
I write 95% of my code in python, I love it, it's my go to language for many things. But for huge code base which I don't master, the lack of type system makes me more than nervous.
