I would imagine this is to make them look less machine-perfect and more "home-made"
If that marketing works on anyone they need to be examined. McDonald's is the definition of machine repeatability.
Except with pickles. They never get the pickles on the actual burger.
That's my guess, too. I live in Japan and eat at fast food places from time to time. One feature of McDonald's is that the food preparation area is almost always visible from the customer area; I can see the people assembling the burgers, handling the fries, etc. At Yoshinoya and other domburi places, even though the shop is much smaller than a McDonald's, I am usually unable to see the person actually putting the rice and toppings into the bowls.
I suspect that efficiency of layout is the top priority in both cases, but I wouldn't be surprised if McDonald's is also consciously trying to show that their food is human-prepared, both in the store design and in their food photos.