It feels like it is over-engineered. If a cheaper charger does the job (assuming it's not so cheap it violates safety regs) isn't this a case of over-optimisation?
PS: I'm not an electronics engineer so please educate me, on why this "filtered" and "cleaner" power supply is necessary to charge a phone?
Bad power really messes with the touch screen. Capacitive touch screens need to sense pico-Coulombs of charger, and this is really hard when the power supply (and the display) create tons of noise. This is a bigger problem as phones get thinner because it's harder to shield the touch screen. For details, see http://www.cypress.com/touch/Noise_Wars_Projected_Capacitanc...
My totally hypothetical theory is that Steve Jobs tried a prototype charger, the touch screen didn't work well, and he said to do whatever is necessary to make sure that didn't happen again.
but that does not help if the customer buys a 2nd 5$ charger and uses that e.g. at work. Then the touchscreen will behave less good and the customer will blame Apple...
Not necessarily the case here, but "go with the cheapest thing that doesn't violate regulations" tends to get combined with "this regulation is inconvenient, let's get rid of it - if it were actually unsafe, nobody would do it" which doesn't end well for anyone (except, maybe, the lawyers).
They link to another tear-down of a fake charger that takes potentially dangerous shortcuts. Also, it generates noise which can interfere with the touch-screen.
PS: I'm not an electronics engineer so please educate me, on why this "filtered" and "cleaner" power supply is necessary to charge a phone?