I plan on buying a 2015 F-150 Lariat in the coming months ... Since the truck will have a full sun/moon roof, the 3 antennas will likely end up on a back-rack...
In addition to the other comments, you should still have room at the rear of the roof for a couple antennas to be properly mounted with NMO's, even with the sun roof. Even if they were right at the rear edge they should work fine, especially for the scanner. The Motos are pretty forgiving as well, it has been my experience that a corner mounted NMO works better than rack mounted antennas plus it will look a lot better.
If you use a multicoupler for the scanners then you only need 2 antennas, otherwise put 3 NMO's in and use the center one for the Motorola.