Dealers get a bonus from the manufacturer for a few different things, like units sold per month, as well as most units sold in their district. So if a large store that does high volume sells you a bike and gets a little below their invoice, they are going to make it up on the other side.
Just like in the car business, it is best to buy your bike on the last day of the month, or the second to the last if you are not able to get to the dealership on the last day. Again, reason is, they need to reach a certain goal in order to get a larger check from the manufacturer.
There are also incentives from the manufacturer that go to the buyer of the bike, sometimes they are incentives or rebates etc, like first time buyers, military, model specific and so on. But remember, you are still taxed on the rebates, or to make it simple, the rebates are deducted from the final, out the door price.
Manufacturers give all sorts of weird stair step or model specific bonuses. So again, this is another reason to go on the end of the month. Let's say a manufacturer puts together a 'salad' where a dealership needs to sell ten R1's, and they will receive an extra $300 per bike, but if they sell 12 R1's, they get $500 a bike, added to all of the other bikes they have sold and will receive money for, I think you will understand why they would take a small hit on either selling the bike or on the trade in by giving a little higher value. Add that to receiving an extra $100 per bike sold because their store sold the most out of their region.
Banks don't usually give money for financing, but what they do a lot of is making deals where say the credit isn't all that great, or bumping a buyer up to a better rate in order to get to a certain payment that a customer needs in order to make a deal, or the finance manager will sell you a maintenance plan or extended warranty and keep your payments the same as you and the salesman worked out.
All in all, it is usually, but not always a good idea to go to a high volume dealership. But as you have read on here about a guy driving from NJ to PA to save a lot of money. One of the main reasons that the deals are better is because the PA dealership is a volume store and makes it up in all directions. Another issue is that Pennsylvania taxes are a lot less than New Jersey taxes. The Jersey dealer needs to hold as much money as possible in order to pay his own bills. Plus I worked and lived in Jersey for too long, and most of those guys are jerks (to put it nicely) and want to try and get over on as many people as possible. (Maybe that is why I sold so many cars and bikes as I did while working there, I wasn't a jerk)