I think there is some truth to what you have said. I would agree that some companies make it easier to order a boat with a certain motor. One of the jokes is that Tritons come with Mercury & Skeeter comes with Yamaha.
Mercury (& Motorguide) do have their sponsored pros but so does Yamaha & Evinrude. Good advertising & discount quantity pricing to the boat manufactures can lead to dominant market share - at least in the bass fishing world. Holeshot & topend are what is important to most bass guys. Those are categories that most people would say Mercury rules. Speaking to a industry rep, where Merc wishes that had a stronger foothold is the saltwater 4-stroke market.
While it is true that Merc has had its problems, they are not alone. Remember when the lower units were blowing up on the 'rudes? Does Merc have more problems or are there just more (individual) cases because there are more of them out there?