As long as you have a regular(quarterly?) check on the drains and make sure water is draining away correctly there is no reason why the roof motor should become waterlogged. It is however not a great design that sites the motor in an area where water is drained, and the relocation of the motor to the nice dry boot, as has been carried out in Germany for many years by enthusiasts, is perhaps where BMW should have installed the unit in the first place.