Roof & Pillar Rebar Damage & Rust Repair Options - Help!

Long story short: About a year and a half ago a chunk of metal rebar dropped off a tractor trailer on the highway and launched towards my car hitting the driver's side windshield pillar and the roof. Recently, Toyota helped me replace the hybrid battery through goodwill, so at this point I plan to keep the car quite a few more years and would like to repair this at the lowest possible cost so it does not eventually rust completely through leading to rain leaking into the car. I went to four auto body repair places today, and gave them the following criteria:

• I do not care about how it looks, I am not worried about resale, I already have 165,000 on the car, I just do not want holes to rust through in the next 3-4 years which will then lead to water getting into the car.

Here were there responses:

• Shop #1: Cost: $50 - Drop it off one day, he will polish (I think he said polish) the area, and then use touch up paint. He said this will really leave it all as is, but it will not rust through.
• Shop #2: Cost: $600 - Remove windshield, metal work on the roof and pillar. Based on my criteria he can cut some corners with the only negative being 3-4 years from now based on sun fading, you may be able to tell the areas that were repaired/painted, as compared to original paint. 3 days of repairs.
  
• Shop #3: Cost $974 - Remove windshield, metal work on roof and pillar. Based on my criteria, he will only paint the affected areas and then fade clear coat instead of newly painting the whole roof. 3-4 days of repairs.
  
• Shop #4: Cost $1,390 - Remove windshield, metal work on roof and pillar. Insisted on repainting whole roof, not only a portion. 4 days of repairs.

See attached pics, shop 2/3/4 are all pretty similar to the attached work quote, just the price difference based on the corner cutting with paint/clear coat.

Is Shop #1's idea too good to be true? My gut is saying go with Shop #2.

Thanks!