Found this after Googling the problem.... it sounds a likely culprit.
"The problem you describe is already known here in Germany. It's caused by defective 'Ãberdruckklappen' (internal pressure flaps?), which prevent/release air pressure when closing (slamming) doors. They are located underneath the rear fenders, hard to locate".
Here's a German thread (perhaps use google-translator ):
http://www.motor-talk.de/forum/wasser-im-fussraum-hinten-rechts-ueberdruckklappen-hintere-radkaesten-defekt-t5513262.html
Seems a few builds did get slightly different flaps (harder) then others; these do not close correctly after a period of time and water from the street get it's way thru fender into the car...
It sounds as though your Mercedes dealer may be telling the truth, although that wont help you with the price .. sorry !