When a device is rebooted or balena systemd service is restarted, all containers are started, even if they were stopped manually.
In some cases it may make sense to permanently disable services if they are not used. Some examples: web server used only for occasional database access, containers providing device drivers, containers used for network troubleshooting, containers providing connection to smart devices or other services, …
There are cases that a service needs to be run only on-demand (e.g. for network troubleshooting) or that a service is part of a release deployed to whole fleet, but only some of the fleet devices use that service (e.g. device drivers).
Being able to permanently disable unused containers would ease up some system resources and could provide better security and stability.