Given that the 4.0L V6 is only 13% smaller in displacement than the 4.6, the V6 Stang has the same axle ratio, wind resistance and weight, then logically a V6 would have at best 13% better gas mileage (Highway constant speed). (Basic physics, an engine is an air pump, displacement determines how much air is pumped, how much air is pumped determines how much gas is needed to maintain the proper A/F ratio).
But since the same HP is needed to move the Stang down the road the V6 has to work a bit harder so the full 13% fuel mileage improvement may not be obtained. In addition when accleration you still have to get the same amount of mass moving. So, I'd expect the V6 to have 10% better gas mileage than the V6 (auto tranny with same 3.31 axle). But the EPA combined mileage is only 7.3% better.
My guess is that the D35 would double the differential, that is it would get about 15% better overall mileage than the 4.0. Which as you say would be very important to many potential Mustang V6 customers.