My dealer's Service Advisor (who I have a very good relationship with) told me that there was no way that my Extended Warranty would cover roof motor replacement if the cause was blocked drain holes.
On the other hand, at least one person on here has persuaded BMW to replace the motor on the grounds that (1) clearing out the drain holes did not form part of any preventative maintenance recommended by BMW and (2) it is not a feasible job to expect the "average" Z4 owner to carry out, especially given how inaccessible one of the drain holes is.
I'd ask your local dealer - it does seem to vary from dealer to dealer.