One of the benefits of the move to app ordering is that I know for certain the order-taker got it right. And I can bookmark the custom order for later reuse.
Now it's just down to the kitchen to fulfill the order correctly, and while it's not 100% it's a lot, lot better.
It's always the kitchen for me across food places (in Australia). Ending up with pickles when I removed them. Ending up with coke zero instead of coke. But the worst is ending up with anything mock meat!
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.