Fuel efficiency goes down with jump range. It's not linear.With or without deep charge, your FSD will still give you the same jump distance per liter of fuel. The boots just allows you to use more fuel on a jump to give you that much more range on a single jump.
Here are two stock Anacondas with roughly the same jump range, one using optimal mass, the other using additional fuel.
Additional fuel only has half the total range, hence half the fuel efficiency.