Apparently a lot of that was due to the location. It is on a hill, and there is a lot more red-tape for hills around here since there are so many more rules. A fair chunk of that was to pay someone with a lot of experience dealing with the zoning board to show up to meetings for you. If you had no life, you could do it yourself. The majority was the actual costs of the permit though.

Having actually done an modification with a permit (installing a new furnace in the exact same place as the old one), I can see why every contracter I talked to said "don't bother with permits" It took about a dozen visits and they rechecked everything each time.

The cost of this particular permit was minimal ($500 US) but I spent so much time driving back-and-forth and waiting on inspectors &ct. that the hassle outweighed the dollar cost.