A great example is the Chef server rpm. It is a 500mb mini distribution in one package. It has copies of perl, python, Ruby, and Erlang in it. If any of these has a security vulnerability, I have to wait on the maintainer to release a new version, and hope it included the security fixes.

They also tend to include things like python header files for no reason. You wouldn't compile against an Omnibus package, but they are there anyway. Examples of this are Sumologic's and Datadog's agents.