Destination & Prep fees are an industry standard and are actually set by the MFG - we charge it on Ducati, Kawasaki, Suzuki also. Some dealers may build them into the price of the bike but that's usually not the case. Some dealers bump the destination fee even more and prep fee goes by hourly service rate so that also differs from dealer to dealer.
Destination is the Alta standard fee which they charge us (dealer) to have the bike shipped to us which is then passed to the customer.
Prep fee is to cover the service time techs take to un-crate and complete the mandatory pre-delivery check list from Alta.
The chargers were made "a-la-carte" to keep the MSRP price down and offer customers an option for a savings. The base charger can be converted from 110 very easily with just a standard wire end from Home Depot.