Could be that having missiles on the inner pylons would affect the airflow to and thus the effectiveness of the aileron (where it is widest) and elevator control surfaces.
Also range could be affected as lift generated by the wing is disrupted more by putting missiles at the longest chord length of the wing vs. where chord length is shorter.
In the picture below only guided bombs are put at the inner pylons. And it seems Indonesia's version of SU27SK version doesn't have the option of any missile or bombs on the inner pylon.
SU-30 loadout
SU-27 loadout