Why does the Configuration Management module warn not to use in production?
As you can see module is in Alpha phase. It's available for community testing so that they can able to fix issues and make it stable.

Every project in Drupal.org go through different phases. Please see more above Project Versions here.

Alpha version refers to 


  These are the first to come out, and are therefore the least stable.
  Most reported errors are resolved but there are most likely still
  outstanding known issues, which might include security issues.
  
  These releases are not yet stable enough for production use, but are
  essential milestones on the way towards the official release. They
  allow a much wider pool of users to test the latest code and provide
  feedback before the official stable release. These releases should
  only be downloaded and used by developers very familiar with Drupal or
  those wishing to help find bugs in the software.


Since Drupal projects entirely community driven, Module maintainers releases projects for testing. Once they are stable you can use them in Production Environment.