If you're getting the bike from a physical store, ask them what the cost differential would be for going with the Continental GP 4000s. They can always resell the stock tires assuming you haven't ridden the bike yet, although they may not be able to sell them as new (possibly sell them as "open box"). I never understood why bikes come without pedals (bike of a certain calibre anyway), but they just include tires like people have absolutely no preference. Tires tend to be one of the things that people are the most finicky and religious about, yet you almost never see a bike sold without tires, unless you are at the point where you buy frame and wheels separately.
This doesn't answer which one is better, but gives you an option for getting the tires you are used to. The LBS should be understanding an accommodate you if you want something that isn't stock on the bike.