which warranty do you think is associated with changing the camera?
besides do you really think that toyota technicians at 3S are smart enough to spot a replaced cam in the same housing?
the technicians at 3S are usually underpaid and work there to learn and leave as soon as they are able to work on their own. they are usually not bothered with going into such details.
also once there is a warranty claim, all 3S have always proven to be very un cooperative and try and come up with lame excuses to avoid warranty claim so incase the camera remains orignal, they will still find some reason to void the claim anyway so upgrading the camera is still better (if required).
Also i have not faced any bad quality issue with 1.6 camera personally.