Does this mean control is going to be observed throughout games from now on?
If I take your meaning to be "will all future COIN games track control at all times?" that is not the case. Each game may keep or alter some mechanics, based on the requirements of the design and the choices made by the designer.
For Cuba Libre I needed a way to allow the Directorio to pursue a course that would not require conflict with the 26 July. Control was an existing mechanic that corresponded closely with DR war aims (at least my best guess about them) and what would be necessary for the DR to claim a victory in the war.