I don't believe the MSRP price includes freight. And, unlike a car, a motorcycle arrives in a crate. It must be removed from the crate and requires some final assembly. Fuel and oil must be added, and the bike needs to be safety tested. So, there is some labor and costs in preparing the motorcycle before customer delivery.
Most, or maybe all motorcycle manufacturers include a couple hours set-up labor into the MSRP. Granted, the labor rate they use is, like for warranty repairs, generally less than that charged by most US dealers. But the cost of setting up a bike, less the allowance provided by the manufacturer, will generally be about 1/3 the labor cost.
At my local dealer, the service dept charges the sales dept the full labor amount for set-up, so service shows a profit. Sales passes those charges on to the customer in order to show the same profit, but money HAS been made, and sales and management already know it.
And, after all that long winded proselytizing, I wouldn't hesitate to pay at least part of the set-up charge on a new model in high demand. The MSRP + set-up is simply a starting point in negotiations. Even if you're starting at invoice, the dealer is fair in getting a little extra profit on popular models.
MSRP doesn't include freight