For scientists, the best method for narrowing down a person's age is a combination of five weighted factors known as the COMPLEX METHOD. It includes analysis of the pubic bones that lie just under the navel along with some vertebral bones, both sets of which start out rough in youngsters but smooth out over time; images of the femur, or thigh bone, which becomes thinner and loses bone mineral over time; dental wear; and closure of the cranium.
Your que. is interesting to the point that the age of the girl is important to analyse the nature of charges filed against accused person(s) but what confuses me is the sentence that you last wrote in very first post because the evidence of her school certificate is shaky hence safely I can say that follow Banda Rape victims (BSP MILA raping a tribal girl in Banda remeber that headlines) evidence case histories where the victim kept on saying she is 17 years whereas the first medical commission verdict said she is 18 years and last Jan. the court appointed second medical commission to determine the very age of the prosecutrix. However the consentual age even as per Hon'ble SC is 16 years in majority of judgments and this ratio carried into your case scenarios I see doubts of conviction however let me also wish your side all the best.