I recently also ran into this problem on the ES350 which my daughter is driving. I used the Rust Removal purchased from Amazon for some rust spots around the roof top , engine hood and trunk top. I wash off the car after sprayed the rust removal and waxed the car 3 times on last Saturday and Sunday. Unfortunately those rust come back with thousands of rust spots and today. I used the rust removal again and add clay to clean those rust spots and add Torque Ceramic Shine and to see if it can give the car better protection. I will put one more layer of ceramic shine on tomorrow to see and keep you posted.
I got other LS460 and Toyota Highlander and only got very few spots not like this ES350 with thousands of rust spots.
Best regards,
Steve Lin