Two things. First, if your dealership has offered free servicing for a specified amount of time where they are providing the products being used for FREE, then yes, they CAN void the warranty if they want to for not using what they recommend, there in lies the niche rule of law. If they however are not providing the products at no cost to you, then no, they can't void the warranty as long as you can show a verifiable maintenance record.
Two, the Motocraft filter, is NOT as good as the others. I will go ahead and put together a true filter specs comparison over the next few days and get the REAL information out there for everyone to see for themselves. But there are vast differences between a lot of the filters on the market and the reason Ford wants you to use the Motocraft filter is because Ford OWNS Motocraft! Nothing more than that, kind of like GM wanting you to use AC Delco products, it is a profit thing for them, not that the filters are better than what is on the market.
I will put something together over the next couple of days and post it in the maintenance area of the forum with the actual specs from the different brands so that everyone can see the real differences.