You cannot incentivise a salesman with a salary. If you were dealing with a Volkswagen direct outlet then they may have used a different system but I doubt it. Even service staff are now targeted to sell this, that and the other. Servicing on my Merc was not too expensive but it would NEVER come...
Depends how new the vehicle is. If serviced and maintained to manufacturer standards then the warranty should not be affected. Reality is that the non franchised dealer will not have access to all the technical info that may be required to service/repair until some years after its first...