I think it really comes down to Python not having a chosen way to handle package management as well as Python being dependent on the underlying C libraries and compilers for the given platform.

Since Python did not prescribe a way to handle it the community has invented multiple competing ways to solve the problem, most of which have shortcomings in one way or another.

To further add to the confusion, most Linux and Unix-based operating systems (Linux, MacOS, etc.) have their own system Python which can easily get fouled up if one is not careful.

This is one place where Java's use of a virtual machine REALLY shines. You can build an uberjar of your application and throw it at a JVM and (barring JNI or non-standard database drivers) it just works. There is also usually no "system Java", so there is nothing to break along those lines.