I was speaking with the local dealer general manager on Saturday. We have a very good relationship.. to the point where if i say I'm going to buy a bike, he holds it for me, period, no q's asked. (I've personally bought 7 from them myself). That being said, the markup on them is typically between 3-500 per bike. that's what the dealer actually makes. I also know the sales manager and , service dept manager (on occasion i get called in to 'consult' on older bikes) , etc. I actually get to see the invoices. Reality is, they will always make some money, but the real profit is service and accessory sales.
What he told me was that there was a customer that he had sold a side by side to out of his area. His area guy had told him he shouldn't sell it to him because the real profit was as said above, in parts/service etc. , and if it was out of area, he'd never see that. Even he was surprised he was told that.
I was in there buying a filter for my CB1100 and looking at a cub for Angie, and we discussed price. They are making $286 bucks profit on that cub at what he quoted me. When you typically see prices at or below msrp, its because they are either making room for new units and have to clear the floor, or trying to reduce the 'floor plan' costs, OR figure they will make it up later on accessory sales. Also, there's incentives for moving X number of units per month/period/year per dealer and this is how they get ranked, from the suppliers, which dictates their ability to get more desirable models, etc.
I've worked in dealerships way back.. automotive. My ex wife was int he Charlotte BMW/Ducati/Triumph dealership for years in administration, her desk was literally 2 feet from the owners and i got to see all sorts of paperwork, etc. They all basically follow the same business model. when this is all understood, It makes navigating a dealership. a bit easier. But it still sucks overall.
In regards to the mfgs driving things ultimately, they aren't there to deal with the general public for the most part. They tell the dealers what to take and not. Proof of that is my '14 CB1100. It was a 4 year old 0 mile bike. Honda had (a bunch) of them sitting in a warehouse for 4 years since the black ones didn't sell as much, they MADE the dealerships take them to sell and they made very little on them because by that point they had depreciated so much . They threw new tires on them, and shipped them out. Some dealers didn't even want them. But when the word got out, they all sold very quick. I paid roughly 1/2 new otd price at the time, dealership made 200 bucks. (i couldn't pass it up).
Point being... find a local dealership. Look for one that probably has made a bunch of money for Honda, they are the best bet on a highly desirable bike.