So using type hints to annotate your flask api, etc. to generate docs is great. No problem.
The issue is that there have been a lot of Java developers switching to Python and they want to pretend that Python is a statically typed language (and use tools like MyPy) because it's more familar to them.
Python is not a statically typed language and treating it as one leads to terrible results. Especially in large projects.
The issue of course if that the Java developers have no point of reference on what a successful large Python project looks like. So they think they are doing great with MyPy when if you compare what they are outputting to a proper large Python project, it's pretty clear they are doing terribly.
When you use Python properly you write self contained microservices. Typing information exists but only on the external interfaces e.g. API. You also don't share business logic code between the self contained microservices because that massively decreases the maintainabily of the overall system. You show your Python code is correct by using Unit Testing and Mocking.
Basically, there is a way to do large Python projects and MyPy (and other static type checking tools) have no place in that story. It only exists to support people in making bad decisions on their codebase.