If it were me, I would be looking for confirmation from another source of those weather strips. Like from Eckler's or Mid America Motorworks. The weatherstrip is supposed to be a SEAL, which implies that it is to keep out water. Holes in a seal kind of defeat that purpose, I would think. I'm sure it wasn't cheap, so having to fill up the holes with silicone or something to make the weatherstrip able to do what you bought it for just seems odd.
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