Gonna get some hate .. but seriously...
Looking at the design Vitus know there is a gap and the Shimano cover plate is not water tight so the connections are. I'd say from a primary design the plastic cover is not to prevent water/dirt ingress but to prevent physical damage to the cables / connections mainly from your feet. Just to be clear water and dirt are not getting into the motor as is being suggested but simply into the outer bash guard casing, under no circumstance should you make a gasket seal from RTV for the bash guard/cable cover its clearly designed to drain.
The standard connections on a DI2 rear derailleur and the computer side connections are totally open to the elements, hence the fancy water tight connectors and they are identical to those inside the bash cover. The power connection IS also a water tight connector. Ultimately if you were not protecting the cables from physical damage the case does nothing.
So ultimately the decision has been made to not block the area off and I agree with them .. why bother. The downside for the consumer is cleaning..
The only design flaw I can see is on the Shimano end and that's the lights connector, presumably if you attach lights and power them you should seal them in also as they could short (Silastic or RTV etc). The design is flexible but surprised they didn't use the same water tight connectors and sell proprietary cables for various sets of lights.
As for W011 errors.. they are thrown when there is something wrong with the speed sensor signal.. say like you when take the signal from the sensor, run it through a cheap RCSC that you power from the light connector so it sends a slower modified pulse rate to the motor than actual. First port of call on fault finding this by myself would be to try removing this "upgrade" and see if the Speed Sensor errors stop