The appraiser is obviously going to charge the borrower for both appraisals.
I wouldn't necessarily assume that the borrower will be charged for both.
I'd do some quick digging and, if the builder is to blame, then the cost of incorrect appraisal is his and shouldn't affect the borrower's side of the GFE or HUD.
If it is the borrower's fault, then they in effect are requesting the second appraisal in order to get you the one you need to approve their loan so yes, it's a valid CC, imo, albeit a contorted one.