The top may have cosmetic damage that may have slipped by "Quality Control" but the top interferes with the front doors! This is a case of a poor quality product installed by a low end business. The expression "You get what you paid for" rings true in this case. The buyer chose a low end supplier to install an inferior product to save money and now is upset that he didn't receive a quality finished product. You received what you paid for not what you hoped you would receive for a discount. A little research shows CCV has had many issues with dissatisfied customers way before this issue began.
I agree that you often get what you paid for, but this is a (roughly) $10,000 top! CCV is not a low end supplier, and they happen to be the only supplier for the Astro/safari as mentioned above. Yes there are numerous documented cases of unsatisfied customers, but also satisfied customers. Additionally, it also sounds like CCV has been making strides on improving the quality control and customer service.
If there is a crease in the mold, you don't need to make a new mold, just do the bodywork to the mold so it quits making that impression that looks like a crack.
The cosmetic nicks and dings in the photo look like they would be best filled with bondo and painted like any other bodywork to me. That shouldn't cost THAT much.
The real issue of concern is how the top overlaps the front doors. That issue looks like it needs to be corrected first, and then the seal replaced since its had a hole worn into it.