The pitchfx system has gotten pretty good, but there's still quite a biti of error in it. Of course there's all sorts of fancy math to make sure that the zone in KC is the same as the one in Toronto, but it's not perfect and it is used to grade umpires.
The umps have gotten a lot better since it was implemented and used to grade them.
Honestly, baseball is a weird sport and I don't mind the different zones for different games. I also don't mind the different ballpark dimensions. Quite frankly, I think it's just as weird that the shape of the playing surface changes, and a team can change the fences, as it is for an ump to call a different zone.
I think the umps were between 97-99% right, btw.