I just received a call from Lexus Canada warranty department (spoke to Ursula Sadiswa).
Their final answer is that they will not replace affected part (rear quarter panel) and only fix the rust spot and repaint it. According to Lexus Canad this is not a manufacturing defect but "environmental damage"!
Ms. Sadiswa declined to comment when asked how environmental damage could cause few rust spots in 6 months old car with only 7000 km on odometer. Her final answer was: "...this is all you are entitled according to Lexus warranty. You can read the warranty manual, it's in your car".
I am taking this issue into the small claims court