I would argue all it shows is they have a very effective strategy for dealing with customers who come back in to the store and are dissatisfied with their original unit.
Within the manufacturing processes, there ARE variations between units, within engineering tolerances, but variances none the less.
They pull some inventory after hand sampling it and those end up as the so called 'brown box' units.
Will they work with their manufacturing partners to decrease the tolerances in the process going forward?
Maybe. I'm sure they have already explored options.
Final decision is always a balance between cost and business impact.
I agree with everything you stated there, assuming that tolerances is the issue here. However, after seeing so many iPad 2's all exhibiting the same type of bleeding (which seems to be pressure induced, as it is not the same kind of flash light bleeding we see in LCD TV's), I'm inclined to believe it is not an issue of manufacturing tolerances, but maybe a fault in the manufacturing process. Whatever Apple is doing to "fix" the brown box return units can most likely be adapted to the factorys is what I'm saying but ultimately that is just an educated guess and my personal opinion.