At least, with java, no one even attempts to use distro package tools to manage libraries, packages and dependencies. Can you see a sysadmin using a syslog replacement implemented in java, requiring java8, along with a webserver only running on java5?
With python, some tools (those big enough to be packaged) are no problem. Some random tool from pip -- not so much -- now you have to patch that python binary, those python dependencies etc... and not just track security.your-distro.org.
It is certainly possible to deploy your system in a similar way you deploy your apps (take on 100% of the burden of maintaining the whole thing) -- but normally you want the "system" to be a stable foundation on which to erect your rickety duct-taped mono-jvm-python-ruby app-stack with the help of puppet/chef/cfengine/salt/ansible... you don't want pip/hackage/gem/npm to manage your system. You might trust it to manage a single application.
You've still got to provision those, but, well, they're individual and isolated and tend not to go hammering into one another. Other than consuming all available system resources.
Oddly: IBM got this right with VM ... 40 years ago?