In either case, you're operating the card outside of the operating range that the warrenty covers. And they can probably tell if that's been done by any damage that may occur (which is really the only reason to worry about the warrenty anyway). Typically computer companies will fab all high-end parts but build in the ability to switch off various components. The ones that make it out without defects get sold as the high-end ones, while the ones that have defects in regions that can be switched off get those regions deactivated and are sold as lower-end parts. Which makes sense, because each fab is expensive as hell to run, and making custom masks for different variants is more expensive than it's worth. The cost of production isn't actually different between different versions of a card, the difference in what you pay for the higher end one is you paying for its fully-functional state; pay less, get a unit with more defects. Simple really.
That's also the reason you can upclock and unlock GPUs to the specs of the top-of-the-line card some of the time. The catch is there's not any assurance that it will work with any given card, or that the operation of the unlocked pipes or whatnot will be 100% correct.
EDIT: Or, as CP points out, it can be done as a marketing decision. If you know that, go for it.
And if you do flash the bios to unlock all of the pipes, it's not necessarily possible to reflash the original BIOS unless you've got it backed up somewhere. A generic one won't necessarily lock the right pipes, if they all have the ability to be disabled.
