I believe this is to "pre boost" during the shift. Logic dictates if you go that high in a gear you want to move fast. So throttle close to give you some boost so next shift don't have lag, at least less. I was confused by this when I put my bov. After some logs and thinking, made sense. So I timed the throttle closure and shifted before opens again and got a nice pull.
Besides, bovs are to release surges and prevent turbo back spin. When the throttle opens and the bov closes. The air flow goes in to the engine, so won't harm the engine.
