There are as many reasons as there are steam locomotives, but if I understand your question correctly, the answer is most likely that the tall and ungainly engines you refer to have a wide firebox and no trailing truck. This necessitates the bottom of the firebox being above the driving wheels. Our GW #90 is like that, and from the side she has quite a bit of space between the wheels and the boiler barrel. Locomotives with trailing trucks or narrow fireboxes that fit between the frames are able to carry the entire boiler lower.