The $500 difference is for more than a lesser paint job and a few odds & ends.
With the BD bike you also need to do your own final assembly and adjustments, or pay a shop to do it for you. With the Giant from a local dealer you will likely get free service on that bike for at least the first year you own it. Warranty issues will be much easier to handle with the Giant (assuming that BD bike even has a warranty). Buying new bikes from local shops often gets you discounts on other accessories you will need with the new bike (helmet, pump, bike shorts/bibs, spare tubes, etc.). Most shops offer free fittings with new bikes. The Giant will surely have a higher resale value should you ever consider to upgrade bikes.