The inner roof panel is a single skin that gets bonded (if you choose) to the outer body along the door edges....so it is sealed from leaking, dust, water, small martial aliens and anything else that may inhabit California from leaking into the cockpit.
The roof line is sloped to the rear as is the inner roof panel...any water will run through into the engine bay....this is a vent/pass through not a snorkel into an airbox...so no issue there.
The rest of the story ,as you put it is upto you...firstly to decide what you want it to do and secondly make any changes you want....
You could always leave the scoop closed and use the inner roof panel to disguise the upper tubes of the cage...(its secondary function)....we dont have the roof scoop functional on either of the race cars....