I am going to leave the question with answer to help anyone who has similar problem with configuring docker and systemd together.
How we can start and stop docker container with systemd?
First we will create docker image
FROM debian:stretch
RUN apt-get update \
&& apt-get install -y systemd \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN rm -f /lib/systemd/system/multi-user.target.wants/* \
/etc/systemd/system/*.wants/* \
/lib/systemd/system/local-fs.target.wants/* \
/lib/systemd/system/sockets.target.wants/*udev* \
/lib/systemd/system/sockets.target.wants/*initctl* \
/lib/systemd/system/sysinit.target.wants/systemd-tmpfiles-setup* \
/lib/systemd/system/systemd-update-utmp*
# systemd should be started with PID 1
CMD [ "/lib/systemd/systemd" ]
Let's build our docker image
docker build -t test_image path_to_docker_file
docker run --name test_container -it -d --privileged --stop-signal RTMIN+3 test_image
docker start test_image
docker exec -it test_container bash
docker stop test_container
IMPORTANT!!!
Do not specify ENTRYPOINT when you start container it should be always SYSTEMD, if you want to execute something do it by attaching to container
docker exec -it test_container bash (or other any commands)
You cannot start systemd during Docker image build.
Solution was tested for Docker version 2.0.0.3 on macOS