I was thinking the same thing about the dealership mats. I just bought an 06 IS 250 last weekend...yep, I'm a newbie and loving it so far. But the dealership did have a flimsy mat with their logo on it right on top of the factory mat...same color and all. I took it out right away but that was just because I do not like promoting a dealership all over my car. I would not be surprised if that was the case too...
On a side note, I have the dealership logo emblem on the back trunk, I have removed these before but I have read about the sensitive paint on a Lexus. Has anyone had issues with removing one from their car?