From looking at the code snippets, a big issue with this study becomes clear - it doesn't reflect how languages like Python are used in practice.
In practice, the "hot loops" of Python are in c/c++/fortran/cython/numba/... i.e. Python code usually makes use of a vast ecosystem of optimized science/maths/data science libraries. Whereas the study code is mainly using pure Python.
It's an issue with the methodology that the programs are written specifically for this study; creating an artificial situation.