I'm not saying it's not clunky, but all in all it's fairly pragmatic. That said, I'm a big Python fan as well. Of all the dynamic languages I work/worked with, it's the one that tries hardest to be less of a footgun, and it has a strong tradition of decent documentation (hear, hear, OCaml library developers...).
I'm not sure I understand. I use the maven shade plugin, so all there is at runtime is the JVM (system package) and the jar (built from libraries, but all of that's handled nicely with maven and its plugins), which can be fetched by http(s) from the repository and then just run (java -jar xyz.jar). There's no wrapping at the filesystem level but there doesn't need to be, because the classpath lets code load everything it needs from within that one jar file.
Shrug; I've found I spend less time debugging non-scala code when working in scala than I spend debugging non-python code when working in python. (When many popular python libraries go wrong, you need to know C).
http://www.allmystery.de/i/t5be775_subgenius_big.jpg
Python with static type hinting is where I want to be.