They are calling it a custom because they are offering it in what they consider a custom stock for the Vanguard. It carries only the standard 1.5" guarantee. The only thing custom about it is a different stock.
http://www.399weatherby.com/_pdf/2008_Full_Line.pdf
I have heard nothing but good things about the Vanguard line; you may also want to look into a Howa as they make the Vanguard for Weatherby. I think though you would be better off getting the Weatherby Sage Country because that stock alone is expensive. You wouldn’t be able to buy a Howa barreled action and the stock for what they are asking for the Weatherby.
J.