Most manufacturers use refurbished units when available. That said, when Epson America refurbs they pretty much remanufacture - and it will have gone through local QA testing, so you are likely to end up with an excellent unit. Given how new the 4900s are, you may well get a new one if it came to it. Something to discuss if that comes to be.
It's bad that the part was damaged - a lot of them are stored not in boxes, but in the plastic bags etc as they come in boxes containing multiples of that part. So most likely it was damaged whilst in the warehouse, but with tens of thousands of line items of spares (if not more), somoene didn't notice it was broken (because they likely didn't know what it should look like). Still, not good.