You answered your own question...it's harder to negotiate on price when making a special order since the dealer doesn't get the same kind of discount versus making an order of several at a time. The advantage is that you get exactly the color/options that you want....as long as you order one of the higher trim levels. For example: you can't order a base LS with options such as foglights, nav and leather....and I believe there are restrictions on the LT1 as well. If you have a good dealership that values your business...they will do the legwork and find a dealership somewhere within reasonable driving distance that has what you want...and do a swap with them.
Also, the biggest disadvantage of special ordering is that you may have to wait weeks or even months before you actually take possession.
Also, the biggest disadvantage of special ordering is that you may have to wait weeks or even months before you actually take possession.