The "custom" part of the US Variax is used more like the way Gibson uses it when they sell a Les Paul Custom. It's not a custom shop in the sense that you call them up or send them an order with exacting specs. You still have to pick from the options that are available, and unfortunately a KOA top isn't one of them. I believe this link has all the variations available (although, the 59P and 69S models aren't listed).

http://www.bananasmusic.com/articledetail.asp/articleid_189/articlename_Line-6-James-Tyler-USA-Custom-Variax-Electric-Guitars-Available-For-Order-Here-At-Bananas