That's based on people's unwillingness to spend time fighting it, which just means they are empowering a city clerk to overrule state law.
I'd personally take it in front of a judge and get the abusing authority to cover the costs. And I'd keep going, because once you get a real judge then you win. It just requires a time investment, but I'm stubborn like that. I'd also ask the court to enjoin the city clerk from enforcing any fees in such a situation. Nothing like delivering a court order to a clerk telling them they can take a hike and reminding them that the term "clerk" in their title is meaningful.