It will still work OK. If the carbs act up (running too rich between 1500-2500 RPM) then you can optionally block off one of the 2 opening inside the box. I'd vote for the front one, as the back one gets less turbulent air. Some have used duct tape to seal off the inside holes: I once pop-riveted a sheet of plastic (0.040" thick) across the front one inside, on a road racer, to get that quiet air from the back.
You could possibly use a large O-ring to fill in the gap: while it is a square cross-section, a large round section will also work. It need not be perfect: I use Walther's Goo glue to hold them in place.