This is just the server disagreeing with both the boss and customer, and then wondering why they might be having a problem with a satisfaction based compensation system.
You're ignoring circumstances where the boss okays the thing but doesn't adjust their perspective and still holds the staff to the same expectations—to deliver as if under the same parameters, when the parameters have obviously changed.
Like I said earlier, it's fine during normal biz hours. But the 30 seconds of extra time the kitchen staff has to put into your special order during a huge rush puts all the orders behind it 30 seconds more behind. So a whole family ordering special orders can hold up 20 people's orders for 5 minutes. And that just builds up the more it happens.
I'm sympathetic with the staff, which in every business takes the bullets for management's decisions. Tech support is similar - frustrated with long wait times? Don't take it out on the person answering the phone; it is management's choice.
It's not just the waitress. It's also the kitchen staff, which has to fulfill the orders. Low-cost special menus like brunch menus make their money on volume. At least half the food service equation relies on the kitchen to whip the orders out in time. Special requests slow the entire kitchen down. Not a problem if, say, there's not a huge rush. But a huge problem if the staff is slammed.
Maybe you should take after the former labor secretary and go try your hand at a service job.