If .pth files are the worst thing you can find to complain about, Python's doing pretty well. That horrific .pth file in question is better placed as the feet of its creators than the mechanism itself.
I searched all my machines and could only find simple ones, all related to some legacy crud for setuptools, one of which was a way to get eggs (which nobody should be using these days) to work.
They're barely a thing these days and mostly a relic from before the end of the Great Setuptools Stagnation and the site package all but discourages their use.
It shows that the language is highly dynamic and you can patch anything? The .pth mechanism allows the party controlling the Python installation (site) to run some init code before any user code, basically an rc mechanism. Nothing more, nothing radical. Maybe you’re unhappy with the dynamism, in which case your complaint is misplaced.