How do the pre-configured ones get from the factory then?
I don't know what the “official” procedure is, but I got a full refund on my BTO 1.6 SSD. I returned it within the 14 days because of the grey lines on the screen, which technically isn't a fault (according to Apple).
Sorry I got a little hyperbolic there - BTO once bitten twice shy
BTOs as already stated are usually excluded from returns for anything other than faulty hardware. The usual "buyer's remorse cooling-off 14-day-period" does not apply.
That they've done this for you, whilst not admitting it's faulty, speaks volumes to me. I'm sure it's been logged and Apple Sales, Techs etc. are being told to admit nothing but 'accommodate' the customer.
That's why, as much as I appreciate it is a pain for most people (me too, I've had to send two back), the more that do, I think the quicker we'll see an end to this screen blight.