The reason they do this (because they don't HAVE to do this) is because of graphical clipping issues with the boots. It looks weird (but acceptable) when boots are worn with greaves because they can poke through.
Personally, I'd like to have both boots and greaves... or at least adding boots to the greave models. It just doesn't look right to me. Luckily, there is an Armor Mod that allows for "thigh guards" which work well with boots.