One possible reasons is that repair fees might not show up in planning the way a guaranteed franchise fee bump would. You can get your franchisees to pay more money if they don't know they are going to be paying it ahead of time, potentially.
If the full extent of the repairs necessitated by the behavior were clear, obvious, and known ahead of time, then yeah, this would strictly be worse. But a slightly lower, but secret, fee might be preferable to a higher but obvious fee.
That's just me speculating though. Could also just be incompetence or maliciousness, or maybe just once upon a time a particular person in McDonalds corporate took a bribe to make it happen. Who knows.