Both the value and the limit of ballistic gel is its uniformity. No two shots into a living body are going to be identical in the tissue interfaces or thicknesses that they cross. Ballistic gel allows valid comparisons between two rounds by eliminating the differences in the routes that they travel through tissues.
Keep in mind that, while 12 inches of penetration in ballistic gel is a common standard, the front surface of the heart is, in most people, only two to three inches deep. I just measured the depth of my own chest at the level of the sternum and it is about 13.5 inches front to back. Thus, a 12 inch standard penetration can account for clothing, possible impact with bone, fat, or a different angle of impact.
Overall, gel isn't perfect, but it is the best current technology for comparison between rounds. The value of gel is in its reproducible results; as has been pointed out, it is not intended to fully mimic an actual shooting result.