I suppose that biochemists chose the standard state to be defined at pH 7 because ΔG°' is closer to the value that a living cell would experience, than ΔG° is. That having been said, there are some sub cellular locations where the pH is considerably different from 7, such as the lysosome and the chloroplast. I can think of several reasons why the two quantities are sometimes numerically different. Imagine we have a simple isomerization, such as HA
HB. If the two pK
a values are different, then the ratio between the total amount of A and the total amount of B will be different at different pH values. The same idea holds true for substitution reactions involving HA and HB. ATP and ADP do not have identical pK
a values, for example.