Most non-tract built new construction is overimproved. That is because by the definition of market value, it is difficult to find data which supports the cost of a custom built new home (most custom builds don't get sold).
One thing that gets me is the term "doesn't appraise". Nothing on the original poster, this term is widely used in the real estate world between agents and loan originators. When I see this language written into contracts I automatically take 10% off of the final value (calm down, I would never do that!)
To me "doesn't appraise" means that an appraisal was not completed. If an appraisal was completed and the indicated value is less than some parties would like for it to be, it still "appraised". Perhaps the contract price or cost is too high?