Kittychan:
The thing with multinational companies (which is effectively what Apple has become since they opened up divisions in different countries) is that they're bound by different national laws; impacted by various international laws as well as treaties; and not every region necessarily has the same policies.
Give you an example, drawing from my experience working at Sony. If you bought a Sony computer in the U.S., we had a tendency to be a little bit more lenient with customers. We would overlook an out-of-warranty repair if it was just some token amount (say, one day, maybe even as much as one week). However, if you bought from Sony U.K., or Sony France, or Sony Europe, the attitude was like, "Hey, in the time it took to get to me on the phone, your warranty lapsed at 12:00 midnight, and it's now like 12:02. Yeah, you're payin' for it, baby." And they flat out just really didn't care. Not trying to say Apple is that harsh, mind you, but just to give you one example.
Now, when comes to both CTO and BTO vs "stock model", it's a pretty standard thing to be stricter with warranty policies, not accept returns so readily, etc. Sometimes, it can be really petty, too. I know a couple examples but won't quote them here as there's no point, it was a different situation, and it was in the U.S., not New Zealand.
Thing is, with custom systems, generally the mfg. will deal with dead units pretty quickly, and will deal with other issues on the basis of how disruptive it is to the purchaser. For them to say, "No, we won't replace it, but yes, we'll replace the defective components," that's a very standard practice, as has been pointed out up-thread. Generally with Apple America, if you take the unit in for repeated service (three times is the typical minimum, and is also an industry standard) they start looking at other options. If it's the exact same problem, they'll probably just replace the system because, at that point, it's cheaper to do. If it's multiple different kinds of problems, well, that's a different road entirely. Mind you, and again I'm talking about dealing with companies here in the U.S., if you can demonstrate a legitimate problematic history (actual component failures, not just cosmetic stuff or that you're just pissed), they'll also explore other options.
In my experience, repeated system failures usually equal a new replacement model, and repeated different subsystem failures equal a refurbished equivalent replacement model.