Which it won't. At least not as a result of me replacing the cover.
There is a reason BMW calls it a "cover" and not a seal. It seals nothing! The seal between the glass and the body is made via the ADHESIVE used to BOND the windshield into the body opening. A good read of the windshield installation procedures in BMW's own service documentation (TIS) shows that this bonding process even contributes to the structural rigidity of the car and can take anywhere from 4 to 20 HOURS to achieve maximum bond.
Like BMW's "lifetime" transmission and differential lubricants, the insistence of the BMW service personnel that the windshield and rear window must be removed and replaced to change the cover(s) SHOULD be taken with a great big grain of salt and not blindly followed just because "they say so".