The 328/quino can't do hundreds of things, run a graphical display well, lots tons of data then upload it to somewhere else or display it graphically.... The Atmel chips are great for embedded custom use, like if this were just going to be a dumb PWM controller, but they don't allow for so many options that a more capable board can do.
As for the voltage issue, a well regulated 3v3 supply is "clean" - the 12v supply in a car is not. It's noisy, prone to wide variation, just a plain old bad environment for delicate electronics, generally.
Why not find an Atmel-based project and posting constructively there, instead of criticizing and asking for justifications in a project that clearly isn't of interest to you?
