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I doubt you lose anything other than the longer waiting time to get one. My iMac and my Macbook are both BTO and they get the same kind of warranty the standard sets offer. I usually order BTO sets thinking the quality control would be higher since its not as easily replaceable as a standard set. So far all my BTO macs have been quite good, so far so good I guess.
 
You can't return it for the normal 14 days, even by paying restocking fee, they won't do it.

Not true, You only can't return if for a refund because you don't like it, but if something if wrong with it you can return it, for a new one or a refund.
 
The main thing that keeps me from doing another one is that, if there's something wrong with the computer, you have to send it back and wait for them to ship you a replacement.

If it's a "standard" configuration, you can simply take it into any Apple Store, and they will give you a replacement on the spot.

I ran into this with a BTO Mini for my parents that was DOA.
 
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