OP here. For all the goodness offered by Docker to deploy apps, sometimes a good old debian package is all that's needed. The format is widely supported and battle-tested, while Docker requires specificities under the form of kernel version, additional software to install, and additional operational knowledge.

In short, if you already have a working Docker installation, you probably don't need PKGR, though nothing prevents you from building your containers by simply apt-get install'ing the app instead of having 10's of RUN commands to install the dependencies.