I think it is to minimise any potential rattle from the fan, and to generally hold it in place. The rubber gasket is pushed down slightly by the bottom cover, which will push against the fan (haven't got one in front of me at the moment, so this is from memory). If this is missing though, it doesn't cause any issues, I think Apple were just being extra cautious.
Apple do a lot of things which don't make sense. For example, the taller logic board screw on A1398 models, which is covered by a rubber component, something else which is easy to lose. The hidden logic board screw on A1425 models and the weird change in battery design. Having no standard USB ports in the new MacBook. The list goes on...
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I don't know......Steve Jobs' obsession with the aesthetics of even the unseen. Sure, Steve's gone, but still. Thanks for the reply.
by Phil