there's always going to be a subjective aspect of something out of the ordinary working for someone, but generally speaking the lower your cuff is, the less support the boot gives, and the more stress that is put on your leg.
think of it this way too... let's say your tongue comes up super high on your leg with only a bit of your shin sticking out the top. Because the top of the boot almost the same height as your shin, your shin can't really flex over the tongue. If your tongue were too low on your leg, your leg would have more potential to flex over the the tongue because it isn't supported as well. That would be rather painful.