We'll accept any container that a Docker registry will; you don't have to use Docker to build your container instance (`flyctl launch` will build an application from a buildpack). You can run systemd in a container.

We don't use Docker to run containers; in fact, we don't run "containers" at all. Instead, we transmogrify OCI containers into root filesystems for Firecracker micro-vms. Your "container" runs as a virtual machine with its own Linux kernel. You can do whatever you'd like with it.

https://fly.io/blog/docker-without-docker/