Winnebago's warranty is only 1 year overall, so that has already expired. The dealer is incorrect. The time left on the Mercedes warranty does make sense from what they quote. We have a 2008 View -H. The -M is what we would buy if our budget would have allowed due to its couch, cabover, dinette and rear bath setup like the -H, but the added bonus in the -M of the dinette and couch on the slide. It seems to me that you are doing the right thing by getting a 3rd party inspection. Even if it is $500, it doesn't seem like a waste of money to do so, especially on what may be your most expensive purchase other than a home. Any items that can be fixed before driving off the lot will be done as a punchdown list. The 90 days is useful insurance too, but a short window to find remaining problems.
http://www.winnebagoind.com/resources/service/ has the warranty information. Each RV we have owned we have uncovered issues after the sale, even from a reputable dealer. In our case the two different dealers made it right, but not all have the service we experienced.
Even with the inspection, there will be things that are missed that you may find later - just like in a home inspection. If you can get a chance to see it after a long rain, that is a good opportunity. I found several RVs we didn't purchase because they had water intrusion issues revealed in the rain. Check out the bathroom skylight area, roof vents, antenna entry points, the cabover, inside all cabinets, etc. for evidence of water. We caught one on a bathroom skylight (crack, hidden) before it became an issue. It was revealed by the dealer doing a leak pressure test when I brought up other issues to rectify and they fixed it (at significant expense to them) at no cost to me.
Welcome to IRV2! We're sure glad you joined the gang! 
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