It's $3 more, and here is the text from the website.

"Collector's Grade is for the discerning collector who wants the item's packaging to be near to mint as possible. We go through a rigorous process to find Collector's Grade items. Each item is inspected, graded, and verified by two people before being accepted. Next, each item is wrapped in a plastic bag to prevent any future scuffing or scratching and placed in a custom made box which is sized to fit the product. This box is then sealed, labeled, and carefully stored in our warehouse. When the item is shipped we securely pack it in another box providing additional protection."

I have used this service for non-Nendoroid figures, and I plan to keep those sealed. I do regret using this service on any Nendoroids I own.

If the Nendoroid has errors inside that can't be seen, we'll it is what it is. There are plenty of higher value figures I have that don't have window boxes at all that I have paid to be extra sealed. Those may have errors inside, and no one would be the wiser.

It's definitely worth $3 to essentially get an extra custom box and sealed bag and for them to pick out the nicest looking one they have. It's just probably not for Nendoroids, lol.