Well, once the Bill is passed by both the Houses, it goes for the Presidential assent. Even if the President returns the Bill for reconsideration of the Parliament, once it is resubmitted by the Parliament without any modifications, the President can do nothing but to sign the Bill, thus making it an Act.
However, certain provisions in the Act can always be challenged in a Court of Law if violating the fundamental rights. In our case, the provision with respect to Rape, I am quite sure, will be struck down by a Court of Law. The reason is simple. There are three classifications of Gender - Male, Female and Others. When we legally change our Gender to Female, the idea of transsexual disappears. The Government itself is recognising us as Female but at the same time going contrary in that clause.
I shall remind you, this is going to be a long drawn battle. Everyone of you, with all the hardwork which is being put right now, are paving way for people like us in the times to come. It will consume decades for complete acceptance. To reach a state of gender diverse community, it will take India more time. However, see the positive side, a decade or two back, we did not have anything. Now, here we are with the help of @orange and @neysara we found our own Website where we all came up together. So, the future is bright and let the smiles on your faces shed light xD