Right now there seems to be no way to create an item that is 3 slots tall and one wide for example. In general, it would be nice if the size could just be input as two numbers within some reasonable limits e.g. max 4x3 (the current grid size of character inventory UI).
One reason for why 1x3 and 3x1 are not the same is because of displaying the items. Some items are tall and slim, and putting them sideways looks ugly.