I don't think the problems the OP mentioned will resolve. Docker is fairly opinionated and so are the authors of it.

If the shoe fits; use it. But Docker is not a 1 size fits all;

  If the idea of trusting a ubuntu image that is debootstrapped from someone on the docker team huzzah
  If the idea of not running being able to run apt-get upgrade and having up to date packages; does not bother you then Docker is for you.

> Note I use Docker and it pains me to keep using it. I feel like I could be trusting Jack the Ripper; or the Pope.