is it even feasible that the clones could have differed in height from each other or Big Boss himself?
Les Enfants Terribles are not all perfect clones of Big Boss. Liquid Snake retains all of Big Boss's dominant genes, whilst Solid Snake has all of the recessive ones.
Further genetic modification was carried out so that one clone would
express each of Big Boss's dominant genes, which were considered to be
inferior soldier genes [if 'super soldier genes' were dominant, this
project wouldn't be necessary], while the other would express his
recessive genes, which were intended to create a genetically superior
soldier. Because of the respective gene expressions, and the
mitochondrial DNA inherited from Dr. Clark's assistant, the twins had
a genetic difference of .43%, enough of a difference to fool nearly
all DNA identification procedures exempting those that used precise
Nine months later, EVA gave birth to the so-called "Twin Snakes": the
clone considered to be genetically "superior", Eli, would later be
known as Liquid Snake, while the "inferior" clone, David, would be
known as Solid Snake.
Solidus is supposedly a perfect clone of Big Boss.
Another clone of Big Boss was later secretly created, this time without modification to dominant/recessive gene expression, thus producing a "perfect clone." This clone would later be known as Solidus Snake (meaning neither solid nor liquid), whom the Patriots would consider a "perfectly balanced masterpiece."
These differences could potentially explain the differences in height.
Source: Games + http://metalgear.wikia.com/wiki/Les_Enfants_Terribles
Alternatively.. differing smoking habits (or other environmental factors growing up) could be the explanation to stunted growth!