This surely is just an important message to first time users... incase there is anyone stupid enough to immerse the phone in water with the flaps open.
You get these type of messages/notifications/tips with windows programs all the time. Tick the box so it doesn't bother you again - I also doubt whether the phone can tell if the flaps are open or shut (hence the initial notification) it almost certainly can't tell - they are just protective covers. This is just a 'take heed' notification. It popped up first time I use my phone - with flaps closed.
I think you are worrying incase the flaps aren't water-tight and a warning message is showing - not the case at all IMO.