> What is the problem actually?

I guess, Lib/test/test_typing.py has gaps in test coverage. The report provided by the OP is a list of random modifications that corrupt logic of Lib/typing.py but still pass all test cases.

Mutation testing is validation of tests themselves. A mutation framework takes code that the validated test actually tests, makes some random but syntactically correct change, and runs the test that should fail some assertion here. If so, the code is rolled back and another mutation attempt is done. If the validated test catches all thousands of such attempts, we can consider it a reliable safety net for any refactoring. Otherwise, we open the report and start to supplement tests and probably package documentation to cover missed scenarios.

Actually, something like cosmic-ray may be added into a CI pipeline, but I suspect that preliminary fixing of test coverage will be a task of the OP themselves. There are no people with enough free time to sit down and sort all tests out, being overwhelmed with new language features, bug fixing and already pending epics of, for example, closing Python internals from extension modules to stop constantly breaking backward compatibility, or fixing startup modules to properly freeze them for speedup of Python launching.