I'm going to go out on a limb here and say depending on how big the whole is there shouldn't be a problem. The "mohican line" is there not only for a little bit of strength, but to hide the body welds. I don't think it will cause the car to collapse upon itself but you might not want to roll it.
Priming the drill holes sounds like a fine idea, and silicone should hold up reasonably well. I'd use housing grade caulk that's made to withstand UV rays.