This is the right answer. My guess is he didn't get the final plan approved or the HOA didn't know how to read plans. If this is the former he is stuck modifying the house to meet the covenants. If he has a plan that matches the house as built with an approval on it from the HOA he has a case ... even if they did screw up. I would sue the HOA for the money to bring my house into compliance if they approved the plan I built from ... with a backup offer of accepting a waiver and they leave me alone but I would not start out with that. The best way to get their attention is to put them in jeopardy of losing substantial amounts of money.