No. I did extensive research to see if painting or anodizing the intercooler would affect the performance. There is so much information out there that proves by doing so it does not affect the performance. I told the dealership my wants of doing so and they did it for me free if cost and I was told it would not void my warranty.
Besides if something happened, Toyota would have to be able to 'prove' that painting or anodizing it caused it to go bad. With so much stuff out there about it not affecting the performance, they would be hard pressed to say otherwise.