I have a very early build 2009 C2S and had some rough running engine performance. I asked the dealer a few months ago to reload the software at the advice of my Ford friend. They complied and did a "long" version reload and the engine is smoother, idles better, and runs a bit more more. Why? I dunno. My Ford friend noted that engineers are constantly tweaking a whole host of parameters and the software loaded into cars is always being updated during production. Unless there is a common complaint such as "rough idling when cold", the factory will not release a bulletin. If you get a reload, you not only get that item fixed, but the cumulative lot of tweaks. Think Windows (I know, that is a bit scary).
So.... while I totally agree with you that something is fake about our cars with these fly-by-wire systems giving us an experience targeted by marketers and realized through software, well.... welcome to this brave new world. There are really few sports cars available any more. I drove a Lotus and was totally in love with the thing for its rawness and mechanical feel.
Look on the bright side.... remember when you could tune your car for high RPM performance or smooth idle? You had to choose. Today, via software, you get both. Not a bad deal actually.
But I agree, some things should be left as a pure mechanical system.
Peace
Bruce