BOVs aren't designed to work with superchargers anyway, they can't constantly flow air, they are made to relieve pressure quickly between a turbo compressor and throttle plate when you lift off. It's been done before as Paul said, they can't flow the air properly, meaning you get a slight pressurisation of the inlet even at idle which will be what affects ecu readings (to the map sensor anyway). Just remove the boost return pipes, blank off the charger inlet and fit an oil catch tank to the oil breather pipe, it's the best way. You get a nice whoosh noise from the boost return valve anyway if it's a noise you are after.
The pipe through the valve cover doesn't need blocking off, it's just a pass through.