Panjo, I have a 640 Duke, which has the airbox as shown in your photo.
Go to bikebandit.com, look up your year model Adv and it will show you the full parts drawing, then compare the Duke to that. To the best of my knowledge, the airboxes are the same....the only reason it would be different is for the subframe. the Adv has a stronger sub-frame (I know this cos I broke my Dukes sub-frame).
The airbox mod is quite common from what i read. In fact, I removed my lid and made a custom screen for it but it broke the screen as it was too fine.
In all honesty, if you have water as high as the top of the airbox, you will flood the motor no matter what the lid looks like.