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There isn't a sensor that will tell you if a cover/flap its closed or not, its just a reminder, it will be wise to get the Dock.
Think about it, if you open and close the usb cover, eventually it will wear off, that might compromise the waterproof, I'm sure they are made to last but its a lot easier to use the dock or you can even buy the magnetic cable on ebay w/o the dock, just a suggestion
With the Z1 the earphone port at the top is open but Sony assured me that it has a waterproof membrain inside which makes it waterproof "but" if you plug in earphones it will not be so dont swim with the earphones in 
Hi dear,
You mean to say this notification is just a notification & it does not mean that any flap is open i.e. something new from Sony to be alert about flap covers
Yes it is just a general notification advising you make sure the flaps are closed, it is not tied to a sensor as outlined by Uliwooly. If you tap the "do not show this again" option when this pops up then you will not see it again.
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