The benefit to costco is you get a 90 day return period. You are right though that you get to choose your colors for type pad and pen. So theres a trade off.
Additionally, for those not wanting to buy the protection plan from Microsoft that increases warranty to 2 years, Costco increases the warranty on computers to 2 years for free, but it doesn't cover accident protection.
Another option for those interested, if you have a Best Buy nearby there is a good chance they will honor your student discount from MS store. You will need to bring in proof. I've been able to use my cell phone on the webpage for proof on other things. Just something to consider.