I'm not sure. I was under the impression that at least some types of permits have to be pulled by a licensed contractor/electrician/plumber. I hope you don't mean the company was going to charge you thousands for just handling the permitting, that's been just a nominal fee when I've had it done, or they don't charge at all. Word to the wise, check to see that permits have been pulled if the contractor said they are doing it. I caught an electrician pulling a fast one in that regard and it almost delayed a house closing.