When I worked a McDonald’s, I didn’t mind special orders when I was working the counter (like FlyingRamenMonster said, it’s just a few extra keystrokes.) But when I was working grill (that is, making the sandwiches) it was annoying only because it interrupted your rhythm. After a while, it was just habit that when you see, for example, a cheeseburger, you add mustard, then ketchup, then onion, then pickle, then cheese. Personally, I had a tendency to screw up special orders because I’d make them like you were “supposed” to without thinking. And then I’d have to make it again. Sometimes more than that (maybe this wasn’t my calling 
) Not only that, but people would get SOOOO upset if you made a mistake.
Course, I got spoiled by being able to make my sandwiches any way I wanted while I worked, so now I amost always special order things when I go there to eat.