Yeah, it has been like that for a while. Granted, about 70% of the price difference (before discounts) is for the operating system. Like the case, power supply, and optical drive, it can be carried forward as you upgrade. RAM and hard drives are sometimes an issue too: I've found that systems vendors tend to charge a lot to upgrade the RAM and hard drive. Often the RAM slots are filled, meaning that you have to replace it if you're doing the upgrade yourself. Many systems don't even have the space to add a secondary hard drive, meaning that you have to replace it if you're doing the upgrade yourself. The list can go on, depending upon your requirements.

Anyhow, at least the options are out there so people can buy what they want and in the form they want: laptops, prebuilt desktops, custom built systems, and home built.