The overwhelming majority of "pain" the author talks about is self-inflicted. The overwhelming majority of Python users are bottom-of-the-barrel worst programmers to walk the face of the Earth. Their problems come from just being really, really bad at what they are supposed to be good at.
So, one complaint you could make is that Python packaging isn't very friendly to incompetent users... well, that's true, but I wouldn't care about that. Quite the contrary: I wouldn't mind it if things were more complex, but worked well, once you mastered them.
Your idea of distributing a single binary is bad for all the reasons I described in the previous post. You just decided that it's not so bad because it helps users who suck to suck less... But I don't want a "solution" that would sacrifice many other desired properties to deal with my potential incompetence. I'd rather learn how to do things right than enjoy being stupid and have someone else cover for my stupidity.