From my personal experience: system languages are really, really good at interacting with operating systems. When you have things deployed on a server that machine generally has one task, and it makes sense to optimize as many layers as possible. For example on a windows system I used MS's `FILE_FLAG_SEQUENTIAL_SCAN` flag to triple read performance; you could of course do the same in python by dipping into ctypes but it doesn't make for a pleasant development experience.
The big trade-off is you're specifying the task more precisely and as a result of that extra labor you get better performance for the life of the tool. SQLITE has a good story of putting together dozens of small optimizations, each <1% performance change, and at the end the library's throughput doubled in pretty much all tests. It's not worth it for research, but it is everywhere else.