I think your veteran installer is spot on. Even from the factory, the design seems to channel water from the upper seal/molding to the sides of the windshield. My installer recommended a different type of upper seal that was flat and 'bridged' the gap. Still not perfect but I think is better.
As for your rust bubbles, I'm positive the rust is much worse once you remove the windshield.
I fear you're correct, I just hope it's not perforating the metal or it will need to go to a body shop. It, my 01LC in the top picture above, had the wide rubber molding on it for years. Once the thinner was installed I saw the bubbling in the paint. Not seeing any chip I thought possibly it was something like sealant under the paint, so I've just been watch, wrong it's rust. After learning from him (veteran installer) I took a second closer look and found it.
I too thought it was a good idea to bridge with wide rubber molding, until I met him. My thinking was it keeps the area sealed from debris and protects from rock chips. He said "paint the chip, open gap is best" as it washes out and doesn't trap moisture. He then showed me the newer cars in the shop all have open gaps, all the way around, with very little molding. They're also installer friendly by being flatter & wider at mounting surface. He then showed me one as the window sealant was being removed by a tech. The tech was able to easily remove all sealant with his raiser tool without a single nick in seconds.
He's explanations of now the manufacture found covering the gap created a cavity that couldn't be washed and held in moisture. That the organic matter in the moisture becomes a acid that eats the paint. He changed my think on the molding and why we are see rust on the 100's. I'll bet we all have some rust or will have regardless if windshield had ever been replaced or not.
A really sweet white 01LX I've been restoring, had the wide rubber filling the gap on it as well. I found the paint was being etched in a line just under the molding along the top. Buffing with a cutting compound helped some, but some was just to deeply etched. It also had rust under the molding that safelite treaded. But believe me not all Safelite tech use proper technics or take the time necessary.
This is a 17 year old 100 with factory glass still in. Edit: Factory glass that was installed by Dealer in year two of it's life. Notice crack has no rock chip along it. That is factory molding which fills half the gap.
Just one more area to be aware of is under plastic molding at bottom of windshield. Not only Acid but Grit builds under there acting like sand paper. Here I cleaned up, remove rust and painted with same black paint (Sika Primer-206 Sticks) Safelite uses. These spots were mostly free of rust but metal was shinny (showing).
This just happens to be picture of the Sika Primer-206 Stix I used under grill and headlights of my 01LC during de-rusting.
