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I'm one of the authors behind Phusion's baseimage.

Phusion's baseimage does not go against Michael Crosby's best practices. His best practices states not to boot init, and with that he means the normal init. He states that not because it's the init process itself that's a bad idea, but because the normal init performs all kinds of work that is either unnecessary or harmful inside a Docker container. In fact, this is exactly what the Baseimage-docker documentation also states: don't use the normal init.

The Phusion baseimage does not contain a normal init, but a special init that is specifically designed for use in Docker.