I don't have any personal experience booking through Travelocity or other travel sites, but I have heard of people scoring some really nice deals on room only reservations.
As far as I know - a reservation is a reservation. Just make sure you are comparing both prices appropriately. For example, check and make sure you are not missing some type of promotion Disney has going on. Also factor in your park tickets, trip insurance (if you plan to purchase), and dining plan (if you plan to purchase).
Good luck planning!
Bottom line - someone gets a commission for your room or package. Sometimes using a TA who specializes in Disney can be the way to go.
As far as Magical Express - I am not sure how that works so perhaps someone else does.