Welcome to the site !!
What they have to "set up" is put the front tire and handlebars on and maybe hook up the battery and the seat (15-30 minutes tops , so unless they are charging $400 in labor to "setup" the bike , it seems excessive to me) .....then fire it up and send it on it's way , not really much considering the extra cost , Like Neil said , $99 even seems excessive since they are getting the bike at "cost" not the retail price they are charging you , so they are already making a decent profit even after paying the manufacturer fees , if at all ..... , if the bike is $3,885 to you , my guess is they more than likely paid $2,500 for it , the rest is simply , as Neil put it ... Fluff ........... If you have any mechanical skills , just tell them you will take it in the crate , the worst you should have to pay is tax/license , etc. ..... If , I end up getting a new bike in the near future , I am going to the dealer and requesting one in the crate ..... I would rather do everything anyway , to make sure it is done right , as well as save the fee's I would be paying , only then to get it home and tear it apart and grease and torque everything correctly anyway ....