Typically, refinancing appraisals are more liberal than home purchase or buy out appraisals.
From what you have described, the appraisal in question come in 'right on the money!'
The reaction to retro-fit observations to justify the undesired outcome is a mistake.
You can choose to have a professional complete an evaluation to determine, from their direct assessment, if you have a legitimate compliant.
You have another option. Select a lender who has a historic record of investing in your community through small business loans, home purchases and refinance. These lenders are 'A' and "B' graded lenders. The too big to fails are all "F" graded along with other predatory companies. Enter your city or zip code and call a few "A" and "B" graded lenders.
Best of success to you,
Annette Lawrence, Broker/Associate
Remax Realtec Group
Palm Harbor, FL