Reviving this thread to document my experience in case it's helpful for other 100-series owners.
Andrey at Super Auto Glass in SF has retired. I requested a quote from Super Auto Glass and was told that they do not work on 100-series windshields any more due to the complexity and risk of damage or finding rust.
The folks at super auto glass were very friendly and apologetic, so props to them on that. They recommended In & Out autoglass in SF. I gave them a call and spoke to one of the installers. He didn't know about the rivets on the side molding and wanted $1000+ for an OEM glass windshield, so I kindly declined to schedule a service. I'm hoping the price was a mistake and not an attempt to gouge.
I then called the local Lexus dealer and asked who they use for glass. They wouldn't provide the company, so that was a dead end. I also called a few of the shops from previous suggestions or the FAQ. Of the shops that knew about the specific issue with our windshields, most were hesitant to offer their services, often insisting I (understandably) send pictures showing no obvious rust.
Because I need to be in Los Angeles in the coming months, I'm just going to wait until I'm there and go to Alfredo's Auto Glass in Corona. He knows what he's doing, deals with everything in-house, and offers fair pricing. Good luck to everyone else on their search.