> Keeping two identical package structures in different places, one for .py files and generated .so files, and one for Cython source files (.pyx, .pxd, .pxi), is not desirable from a user perspective, and would require namespace packages for the lookup, where otherwise a simple single Python package structure would suffice. That would complicate Cython's internal compile time import lookup system quite a bit.

This is an important point. You shouldn't consider these Cython files as "extra stuff", they really should be considered as part of the package.