Currently all Process actions are available to the user and there's no indication during development that the created Process Flow is a valid System Flow. There's a validation that tells if there are Process actions used that are not available to be used in System Flows but it lacks helping the developer successfully set up a System Flow.
With a checkbox in the main Process Flow screen, not only will it be easy to find System Flows in the long list of Process Flows, it can also be the indication for the SF to limit the amount of Process actions available for use. Also the Process schedule tab can then be hidden for Process Flows whilst available for System Flows.
When changing an existing Process Flow to be a System Flow, there could be a check upon switching the checkbox if there are Process actions used that are not supported. When true, show a message.