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If your joints don't meet up then you hope the bead on the glass somehow diverts the water correctly or you will have ever ounce of water that comes down the rail enter into the cabin area !!
Full bead on the glass is best but you do need to make sure beads line up and you don't create a headache for yourself with huge glob of urethane at the joints for your next replacement in a few years on the same job especially if your doing fleet trucks/cars
I use a yellow grease pencil and measuring tape. Using VIN window as starting point I measure old W/S every 6" and transfer to new glass; never had a problem. I also made a couple of patterns from clear plastic that I could tape in place to mark the line, worked great for the DW1640 when they were popular.