When running stubtest from the master branch on scipy-stubs (31 errors) and the numpy stubs from numtype (195 errors) there are a bunch of new errors about missing @disjoint_base, for example:

error: numpy.random.RandomState is a disjoint base at runtime, but isn't marked with @disjoint_base in the stub
Stub: in file src/numpy-stubs/random/__init__.pyi:77
<TypeInfo numpy.random.mtrand.RandomState>
Runtime:
<class 'numpy.random.mtrand.RandomState'>

I think it's a good check, but I'm a bit hesitant to add it before PEP 800 is accepted. Because if it were to be rejected, and typing_extensions.disjoint_base were to be removed, then I'm sure you can see how that could cause a bunch of problems.