Well, you're caught between a rock and a hard place, IMO; if you (rightly) complain, out comes the bureaucratic tape and they could delay you indefinitely.
I remember years ago when we were fixing our front porch steps and we had the GALL to complain about a city water main leak that was damaging the asphalt in front of our house. The city was there within hours - NOT to take a look at the leak but to ask if we had a permit for "remodeling" the porch.
You give a little bit of power to some of these pencil pushers and they have a field day pushing your buttons, like tin-horn dictators.
I hope you get the license this month, good luck.