Not sure mine is done right but mine does not cover the holes. I will have to take a picture, I do not have a close up. The diagram in the FSM does not show that happening but if the trim still fits over everything then I do not see where there is any problem.
Click on the attachment. It shows the glue being masked off on the bottom of the outside edge of the gutter. That is where I cut it off after putting a bit of silicon seal around all the edges except the windshield and rear reveal. I will do them later. I put a real light amount with a tooth pick where it was exposed between the trim on the sail panels. I will finish sealing the rear when I get ready to put the trim on so the trim will hold it in place while it dries.