I don't dispute that it works. But it does rather detract from, well, the aesthetic elegance of the machine. Apple has these fancy backlit keyboards--it's a great shame to make the keycaps wrong.
Plus, it also causes big problems when I let others use my machine. Hunt-and-peckers don't stand a chance when your keys are mismatched. Though they probably struggle even with the regular Apple layout--good luck finding # on the keyboard, since Apple doesn't deign to print it. Sure, once you know it's option-3 it's not so bad, but I don't know how you're meant to just figure that out for yourself.
And the thing is, it's all just gratuitous. Apple's layout isn't in any meaningful sense better. It's just... different.
Is this only an issue with a US keyboard layout perhaps (I've a Dutch layout)?
UK keyboards on PCs have a dedicated key for #/~, " is shift-2 and @ is shift-'. £ (currency symbol) is shift-3.
On a Mac the " and @ are the wrong way round (shift-' and shift-2 respectively), and the key that should produce # instead generates \. The only way to get a # is option-3, which is not marked on the keys. The Mac "UK" layout is basically the US layout with £/# reversed.