Ford is not going to let you "upgrade" your battery under warranty. They installed the larger packs when they were unable to source the smaller ones. So it would work like this:
Is your battery failed in a way that warrants replacement, according to Ford's guidelines? If not, any replacement it upgrade would be out of pocket and full price. Capacity loss has to be significant to qualify on it's own, not sure if it's officially codified.
If they do consider it failed and will replace it under warranty, do they have the smaller pack available? If so, that is what you get. You can't "pay the difference" to upgrade (I tried this very thing before I ended up with the larger pack)
If they only have the larger one and they're replacing it under warranty, awesome. But that's the only way it can happen without you buying the whole thing yourself.
Also, what's the actual mileage you get from a charge? Not what the meter says, but real miles going from full to almost empty?
2012 Candy Blue FFE
33.5kWh battery pack
CHAdeMO DC Fast Charging