This is incorrect. It’s an immutable OS. But containers can be started and stopped as much as you want. It’s the sole purpose of Flatcar.

There are multiple ways to start containers, one of them is to define systemd units in Ignition. If that part needs to change, reprovisioning is needed but a new "flatcar-reset" tool (in Alpha) should make the barrier for reprovisioning lower by only requiring a reboot and being able to keep wanted local data. In the past Ansible was a common choice if neither Kubernetes, Nomad or even docker compose are used.

No not quite. You can even add new systemd units at boottime - there’s a special ignition config for that