Nothing in biology is exactly the same - or said another way, biology is optimized at many different scales - from basic (even quantum) physics, all the way up to social adaptations. So screwing with codons could have very subtle effects that have nothing to do with the physical design of the organism, but nonetheless affect its size and growth rate. Off the top of my head, to give some random examples - the locations on the genome of two metabolic enzymes have been shifted by what amounts to a few nanometers, and that affects metabolic flux, or the DNA now has more purines in a row than before and that causes some charge buildup that calls in DNA repair mechanisms slightly more often and disables transcription slightly more, or the genome when folded up is slightly more rounded than oblong because of strange sterics, or any number of very weird optimizations all the way down the physical causal ladder.