[pile o' wrx]

The metal is painted (which will protect it from rust, as well as the clearcoat). Silicone will stop moisture from getting to the metal, which will also help against rust. I don't think I have ever seen evidence of silicone causing rust. I siliconed mine in, and it did the trick. Clean to this day...

True. But if you have a leak coming from elsewhere, now you've just created an area where the moisture can sit undisturbed and allowed to do it's thing on your panel.